Pawan Kumar wrote:
Respected Sir,
Greetings from Pawan.
1. Were there gaps between the water and lipid headgroups? If so,
the lipids may be pulling towards the solvent. Restrain the lipids
and run an equilibration for a longer time.
Gap was there when I used a value of 0.5 in the vdwradii.dat file. The
gap reduced as I decreased the value from 0.5 to 0.35 to the default of
0.15. I tried all the three possibilities.
When I used the default vdwradii.dat file and made the solvation
followed by simulation runs the lipids didnt pull apart. But there were
water molecules on the sides of the bilayer and not in the interior.
This indicates to me that the gaps are causing the problem. Do not run
simulations with water in or around the lipids; it is not realistic. You can
clean up such a starting structure, either by some clever script like those on
the wiki, or by looking at the structure, taking note of which water molecules
are offending, and deleting them manually from the coordinate file.
The other option is to temporarily give genbox a box that is slightly smaller in
the x-y dimensions, so that it will try to place less water around the POPC
periphery.
2. 5000 steps is far too short to expect any realistic behavior for
lipids. Equilibration can take upwards of 10-20 ns.
As per your suggestion I have made the final mdrun now again with 500000
steps. Hopefully this will work.
3. You haven't mentioned the contents of your .mdp file. Maybe
you're doing something wrong.
I am using the same .mdp file which I posted before. I have just removed
the restraints.
I don't have record of the previous email; as a general guide, post the .mdp by
default when experiencing weird behavior. That way the users on this list won't
have to go combing through the archive to find it. If you want free help, make
it easy to help you :)
-Justin
4. Are you using Gromos/Berger or OPLS/converted Berger for your
system? There have been so many of these questions from different
users over the last few days that it's hard to keep track. If you
are using OPLS/converted Berger you may have made a mistake in
translating the C6/C12 parameters.
I am using gromos 96 force field (G43a1) and as per your suggestion I
have edited the lipid.itp file to remove the part containing "
lipid-gromos interactions".
Thanking you,
Yours sincerely,
Pawan
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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