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pbc box
- imankatouzian
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4 years 1 month ago #8443
by imankatouzian
pbc box was created by imankatouzian
Dear all,
In the simulation of my protein in water.gro (downloaded for CG) when I get my file solvated.gro as I open it in vmd file I notice that my protein is out of the box what should I do in this respect as I did not have this problem when simulated in all-atom mode?
Also, when I want to neutralize my system, should I do this as in all-tom by
the codes I run in all-atom mode?
gmx grompp -f MDP/ions.mdp -c solv.gro -p topol.top -o ions.tpr
gmx genion -s ions.tpr -p topol.top -nname NA -nn 7 -o solv_ions.gro
So, it is right if I do it after the minimization-vacuum step?
Thanks.
In the simulation of my protein in water.gro (downloaded for CG) when I get my file solvated.gro as I open it in vmd file I notice that my protein is out of the box what should I do in this respect as I did not have this problem when simulated in all-atom mode?
Also, when I want to neutralize my system, should I do this as in all-tom by
the codes I run in all-atom mode?
gmx grompp -f MDP/ions.mdp -c solv.gro -p topol.top -o ions.tpr
gmx genion -s ions.tpr -p topol.top -nname NA -nn 7 -o solv_ions.gro
So, it is right if I do it after the minimization-vacuum step?
Thanks.
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- riccardo
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4 years 1 month ago #8448
by riccardo
Replied by riccardo on topic pbc box
Regarding the out-of-the-box "problem": see
cgmartini.nl/index.php/component/kunena/...entering-the-protein
. I bet as soon as you run a short minimization/MD simulation, you won't have this "problem" anymore.
Your commands for the neutralization of the system look fine.
Regarding whether to perform the minimization in vacuum in the case of Martini: the tutorial ( cgmartini.nl/index.php/tutorials-general...n-gmx5/proteins-gmx5 ) suggests a *very* short one (10-100 steps), but I know of a lot of people which just skip this altogether with Martini and just go for a minimization in the solvent. You can try both, and maybe there won't be any differences.
*Please* don't spam the forum with the same messages in multiple threads (see your new post here: cgmartini.nl/index.php/component/kunena/...ater-out-of-box#8446 )
Your commands for the neutralization of the system look fine.
Regarding whether to perform the minimization in vacuum in the case of Martini: the tutorial ( cgmartini.nl/index.php/tutorials-general...n-gmx5/proteins-gmx5 ) suggests a *very* short one (10-100 steps), but I know of a lot of people which just skip this altogether with Martini and just go for a minimization in the solvent. You can try both, and maybe there won't be any differences.
*Please* don't spam the forum with the same messages in multiple threads (see your new post here: cgmartini.nl/index.php/component/kunena/...ater-out-of-box#8446 )
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- imankatouzian
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4 years 1 month ago #8451
by imankatouzian
Replied by imankatouzian on topic pbc box
Thank you riccardo,
as I tried to build minimization.tpr file using :
gmx grompp -f minimization.mdp -c solv_ionsCG.gro -p system.top -o minimization.tpr
I received this error :
ERROR 1 : No such moleculetype NA I want to inquire how should I define NA milecule in my martini.itp file which is written below : ;;;;;; WATER (representing 4 H2O molecules) [ moleculetype ] ; molname nrexcl W 1 NA 14 [ atoms ] ;id type resnr residu atom cgnr charge 1 P4 1 W W 1 0 ;;;;;; ANTIFREEZE (prevents freezing of water) [ moleculetype ] ; molname nrexcl WF 1 [ atoms ] ;id type resnr residu atom cgnr charge 1 BP4 1 WF WF 1 0 Many thanks.[file system.top, line 15]:
No such moleculetype NA
I want to inquire how should I define NA milecule in my martini.itp file which is written below :
;;;;;; WATER (representing 4 H2O molecules)
[ moleculetype ]
; molname nrexcl
W 1
NA 14
[ atoms ]
;id type resnr residu atom cgnr charge
1 P4 1 W W 1 0
;;;;;; ANTIFREEZE (prevents freezing of water)
[ moleculetype ]
; molname nrexcl
WF 1
[ atoms ]
;id type resnr residu atom cgnr charge
1 BP4 1 WF WF 1 0
Many thanks.
as I tried to build minimization.tpr file using :
gmx grompp -f minimization.mdp -c solv_ionsCG.gro -p system.top -o minimization.tpr
I received this error :
ERROR 1 : No such moleculetype NA I want to inquire how should I define NA milecule in my martini.itp file which is written below : ;;;;;; WATER (representing 4 H2O molecules) [ moleculetype ] ; molname nrexcl W 1 NA 14 [ atoms ] ;id type resnr residu atom cgnr charge 1 P4 1 W W 1 0 ;;;;;; ANTIFREEZE (prevents freezing of water) [ moleculetype ] ; molname nrexcl WF 1 [ atoms ] ;id type resnr residu atom cgnr charge 1 BP4 1 WF WF 1 0 Many thanks.[file system.top, line 15]:
No such moleculetype NA
I want to inquire how should I define NA milecule in my martini.itp file which is written below :
;;;;;; WATER (representing 4 H2O molecules)
[ moleculetype ]
; molname nrexcl
W 1
NA 14
[ atoms ]
;id type resnr residu atom cgnr charge
1 P4 1 W W 1 0
;;;;;; ANTIFREEZE (prevents freezing of water)
[ moleculetype ]
; molname nrexcl
WF 1
[ atoms ]
;id type resnr residu atom cgnr charge
1 BP4 1 WF WF 1 0
Many thanks.
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- riccardo
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4 years 1 month ago #8453
by riccardo
Replied by riccardo on topic pbc box
You need to include the ions itp (get it here:
cgmartini.nl/index.php/force-field-parameters/ions
) in your top file, e.g. your system.top should contain:
#include "martini_vXXX.itp"
#include "martini_ions.itp"
#include "whatever_other_topology_you_need.itp"
[ moleculetype ]
; molname nrexcl
W 1
NA 14
...
#include "martini_vXXX.itp"
#include "martini_ions.itp"
#include "whatever_other_topology_you_need.itp"
[ moleculetype ]
; molname nrexcl
W 1
NA 14
...
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