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water
- syahidah
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12 years 3 days ago #935
by syahidah
water was created by syahidah
hi,
greeting all MARTINI users,
i have few questions.
1)may i know the water.gro in tutorial folder is the coarse-grained one or we have to coarse-graining it? can i use it straight away after downloading it?
2)do we need to reduce the number of water molecules if we use the coarse-grained one?
3)how can i get the anti freeze particles?
thank you,
your kind co-operation are much appreciated,
best,
syahida
greeting all MARTINI users,
i have few questions.
1)may i know the water.gro in tutorial folder is the coarse-grained one or we have to coarse-graining it? can i use it straight away after downloading it?
2)do we need to reduce the number of water molecules if we use the coarse-grained one?
3)how can i get the anti freeze particles?
thank you,
your kind co-operation are much appreciated,
best,
syahida
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- jantunes
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11 years 11 months ago #936
by jantunes
Replied by jantunes on topic water
Hey,
1) water.gro is a box with 400 martini (CG) waters. If you open it with emacs or vmd you will see only one atom per water (atom name - W). So yes u can use it straight away ;)
2) 1 martini water = 4 atomistic waters, so p.e. if u want 40 atomistic waters per lipid (to reproduce something) you just need to have 10 martini waters per lipid
3) For that I just change the group name of the last 10% waters (in .gro file) from W to WF
Cumps,
Jorge
1) water.gro is a box with 400 martini (CG) waters. If you open it with emacs or vmd you will see only one atom per water (atom name - W). So yes u can use it straight away ;)
2) 1 martini water = 4 atomistic waters, so p.e. if u want 40 atomistic waters per lipid (to reproduce something) you just need to have 10 martini waters per lipid
3) For that I just change the group name of the last 10% waters (in .gro file) from W to WF
Cumps,
Jorge
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- syahidah
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11 years 10 months ago #970
by syahidah
Replied by syahidah on topic water
thanks Jorge;)
i try to insert the water by using genbox
(genbox -cp em1.gro -cs water.gro -o waterbox.gro -maxsol 750)
the water molecules however, were not in random configuration but located at the edge of the box in a cubic shape manner..
i wonder why did the water molecules were not in random configuration..
i tried using -ci but failed...
could you help me..
i try to insert the water by using genbox
(genbox -cp em1.gro -cs water.gro -o waterbox.gro -maxsol 750)
the water molecules however, were not in random configuration but located at the edge of the box in a cubic shape manner..
i wonder why did the water molecules were not in random configuration..
i tried using -ci but failed...
could you help me..
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- djurre
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11 years 10 months ago #972
by djurre
Replied by djurre on topic water
To check for overlap between atoms genbox uses the parameter '-vdwd'. The standard value is for atomistic system. Change it to 0.21 for Martini system.
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- syahidah
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11 years 10 months ago #995
by syahidah
Replied by syahidah on topic water
Dear djjure,
Thanks alot for your suggestion,Thank you so much!really appreciate it.
Thanks alot for your suggestion,Thank you so much!really appreciate it.
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