- Posts: 12
Backward Mapping for lipid (CHOL): cannot compile
- hind
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2 years 9 months ago #9038
by hind
Replied by hind on topic Backward Mapping for lipid (CHOL): cannot compile
Thank you so much.
first step works and generate all files.
but how can modfiy backward.py to use tip3 for water instead of sol?
Regards,
Hind
first step works and generate all files.
but how can modfiy backward.py to use tip3 for water instead of sol?
Regards,
Hind
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- Pham
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2 years 9 months ago #9040
by Pham
Replied by Pham on topic Backward Mapping for lipid (CHOL): cannot compile
Depending on your #include water model in topol, it will read it.
I use tip3p and still declare as SOL in topol's [molecule] (since the tip3p.itp named it SOL). Just need to #include whatever atomistic FF parameter for the water you want, I guess.
I use tip3p and still declare as SOL in topol's [molecule] (since the tip3p.itp named it SOL). Just need to #include whatever atomistic FF parameter for the water you want, I guess.
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- hind
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2 years 9 months ago #9041
by hind
Replied by hind on topic Backward Mapping for lipid (CHOL): cannot compile
Thanks
i added #include "../charmm36-feb2021.ff/tip3p.itp" and it works.
but I got this error at nvt step (gmx grompp -f 3-mdpr-0.00002.mdp -c 2-EM.gro -r 0-backward.gro -p backmapped.top -o 3-mdpr-0.00002 -maxwarn 2
gmx mdrun -deffnm 3-mdpr-0.00002 -v -nt 0 )
Fatal error:
Step 0: The total potential energy is 8.96017e+13, which is extremely high.
The LJ and electrostatic contributions to the energy are 8.96017e+13 and
-472998, respectively. A very high potential energy can be caused by
overlapping interactions in bonded interactions or very large coordinate
values. Usually this is caused by a badly- or non-equilibrated initial
configuration, incorrect interactions or parameters in the topology.
####
i change emstep to 0.001 in initram.sh and dt of nvt to 0.00002 but still the same error.
any suggestion to fix it. I would be grateful
i added #include "../charmm36-feb2021.ff/tip3p.itp" and it works.
but I got this error at nvt step (gmx grompp -f 3-mdpr-0.00002.mdp -c 2-EM.gro -r 0-backward.gro -p backmapped.top -o 3-mdpr-0.00002 -maxwarn 2
gmx mdrun -deffnm 3-mdpr-0.00002 -v -nt 0 )
Fatal error:
Step 0: The total potential energy is 8.96017e+13, which is extremely high.
The LJ and electrostatic contributions to the energy are 8.96017e+13 and
-472998, respectively. A very high potential energy can be caused by
overlapping interactions in bonded interactions or very large coordinate
values. Usually this is caused by a badly- or non-equilibrated initial
configuration, incorrect interactions or parameters in the topology.
####
i change emstep to 0.001 in initram.sh and dt of nvt to 0.00002 but still the same error.
any suggestion to fix it. I would be grateful
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- Pham
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2 years 9 months ago #9048
by Pham
Replied by Pham on topic Backward Mapping for lipid (CHOL): cannot compile
Did it actually goes thru all the EM steps? In other words, what is the value of final step it calculated in 1-EM and 2-EM?
If it actually finished running all 500 steps of 1-EM and 2-EM, you can considered increase the steps using -em and -nb flags and test out.
If it stop at a few steps in 2-EM with F_max is inf (infinite), then consider rerun it multiple times (and possibly try to change the -kick to 0.07 or some thing). I ran into this problem for my system. Some time, I got luck and run thru every thing for the 1st time. Some other times, I have to run 5 times to have the final aa result.
If it actually finished running all 500 steps of 1-EM and 2-EM, you can considered increase the steps using -em and -nb flags and test out.
If it stop at a few steps in 2-EM with F_max is inf (infinite), then consider rerun it multiple times (and possibly try to change the -kick to 0.07 or some thing). I ran into this problem for my system. Some time, I got luck and run thru every thing for the 1st time. Some other times, I have to run 5 times to have the final aa result.
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- cneale
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2 years 8 months ago #9086
by cneale
Replied by cneale on topic Backward Mapping for lipid (CHOL): cannot compile
Changing the kick value may be a red herring unless you verify that your version of the code actually uses it:
www.cgmartini.nl/index.php/component/kun...-silently-turned-off
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