Hello Sir,<br><br>Can you please tell me how to couple ions with SOL ?<br>Is there any command in gromacs to do that ?<br><br>Thanking you,<br>Pawan<br><br><div class="gmail_quote">On Tue, Apr 7, 2009 at 9:44 AM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Pawan Kumar wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im">
Respected Sir,<br>
<br>
Greetings from Pawan.<br></div><div><div></div><div class="h5">
Sorry for the inconvenience about the .mdp file.<br>
The mdp file used for the final run is<br>
*_<br>
final.mdp file_*_<br>
<br>
_title = Protein in POPC bilayer<br>
cpp = /usr/bin/cpp<br>
constraints = all-bonds<br>
constraint-algorithm= Lincs<br>
integrator = md<br>
dt = 0.002 nsteps = 5000 nstcomm = 1<br>
nstxout = 50<br>
nstvout = 1000<br>
nstfout = 0<br>
nstlog = 10<br>
nstenergy = 10<br>
nstlist = 10<br>
ns_type = grid<br>
rlist = 1<br>
coulombtype = PME<br>
rcoulomb = 1<br>
vdw-type = Cut-off<br>
rvdw = 1<br>
; Berendsen temperature coupling is on in two groups<br>
tcoupl = berendsen<br>
tc_grps = Protein POPC SOL CL-<br>
tau_t = 0.1 0.1 0.1 0.1<br>
ref_t = 300 300 300 300<br>
</div></div></blockquote>
<br>
Don't couple ions seperately. See <a href="http://wiki.gromacs.org/index.php/Thermostats" target="_blank">http://wiki.gromacs.org/index.php/Thermostats</a><br>
<br>
Mark<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><div></div><div class="h5">
; Energy monitoring<br>
energygrps = Protein POPC SOL CL-<br>
; Pressure coupling is on<br>
;Pcoupl = berendsen<br>
tau_p = 2.0 2.0<br>
compressibility = 4.5e-5 4.5e-5<br>
ref_p = 1.0 1.0<br>
Pcoupl_type = semiisotropic<br>
; Generate velocites is on at 300 K.<br>
gen_vel = yes<br>
gen_temp = 300.0<br>
gen_seed = 173529<br>
_*<br>
mdp file for position restraint mdrun*_<br>
<br>
title = Protein in POPC bilayer<br>
cpp = /usr/bin/cpp<br>
define = -DPOSRES -DPOSRES_LIPID<br>
constraints = all-bonds<br>
constraint-algorithm= Lincs<br>
integrator = md<br>
dt = 0.002 nsteps = 5000 nstcomm = 1<br>
nstxout = 50<br>
nstvout = 1000<br>
nstfout = 0<br>
nstlog = 10<br>
nstenergy = 10<br>
nstlist = 10<br>
ns_type = grid<br>
rlist = 1<br>
coulombtype = PME<br>
rcoulomb = 1<br>
vdw-type = Cut-off<br>
rvdw = 1<br>
; Berendsen temperature coupling is on in two groups<br>
tcoupl = berendsen<br>
tc_grps = Protein POPC SOL CL-<br>
tau_t = 0.1 0.1 0.1 0.1<br>
ref_t = 300 300 300 300<br>
; Energy monitoring<br>
energygrps = Protein POPC SOL CL-<br>
; Pressure coupling is on<br>
;Pcoupl = berendsen<br>
tau_p = 2.0 2.0<br>
compressibility = 4.5e-5 4.5e-5<br>
ref_p = 1.0 1.0<br>
Pcoupl_type = semiisotropic<br>
; Generate velocites is on at 300 K.<br>
gen_vel = yes<br>
gen_temp = 300.0<br>
gen_seed = 173529<br>
<br>
<br>
Thanking you,<br>
<br>
Yours sincerely,<br>
Pawan<br>
<br></div></div><div><div></div><div class="h5">
On Mon, Apr 6, 2009 at 5:35 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
Pawan Kumar wrote:<br>
<br>
<br>
Respected Sir,<br>
<br>
Greetings from Pawan.<br>
1. Were there gaps between the water and lipid headgroups?<br>
If so,<br>
the lipids may be pulling towards the solvent. Restrain the<br>
lipids<br>
and run an equilibration for a longer time.<br>
<br>
Gap was there when I used a value of 0.5 in the vdwradii.dat<br>
file. The gap reduced as I decreased the value from 0.5 to 0.35<br>
to the default of 0.15. I tried all the three possibilities.<br>
When I used the default vdwradii.dat file and made the solvation<br>
followed by simulation runs the lipids didnt pull apart. But<br>
there were water molecules on the sides of the bilayer and not<br>
in the interior.<br>
<br>
<br>
This indicates to me that the gaps are causing the problem. Do not<br>
run simulations with water in or around the lipids; it is not<br>
realistic. You can clean up such a starting structure, either by<br>
some clever script like those on the wiki, or by looking at the<br>
structure, taking note of which water molecules are offending, and<br>
deleting them manually from the coordinate file.<br>
<br>
The other option is to temporarily give genbox a box that is<br>
slightly smaller in the x-y dimensions, so that it will try to place<br>
less water around the POPC periphery.<br>
<br>
<br>
<br>
2. 5000 steps is far too short to expect any realistic<br>
behavior for<br>
lipids. Equilibration can take upwards of 10-20 ns.<br>
<br>
As per your suggestion I have made the final mdrun now again<br>
with 500000 steps. Hopefully this will work.<br>
<br>
<br>
3. You haven't mentioned the contents of your .mdp file. Maybe<br>
you're doing something wrong.<br>
<br>
I am using the same .mdp file which I posted before. I have just<br>
removed the restraints.<br>
<br>
<br>
I don't have record of the previous email; as a general guide, post<br>
the .mdp by default when experiencing weird behavior. That way the<br>
users on this list won't have to go combing through the archive to<br>
find it. If you want free help, make it easy to help you :)<br>
<br>
-Justin<br>
<br>
<br>
4. Are you using Gromos/Berger or OPLS/converted Berger for your<br>
system? There have been so many of these questions from<br>
different<br>
users over the last few days that it's hard to keep track.<br>
If you<br>
are using OPLS/converted Berger you may have made a mistake in<br>
translating the C6/C12 parameters.<br>
<br>
I am using gromos 96 force field (G43a1) and as per your<br>
suggestion I have edited the lipid.itp file to remove the part<br>
containing " lipid-gromos interactions".<br>
<br>
<br>
<br>
Thanking you,<br>
<br>
Yours sincerely,<br>
Pawan<br>
<br>
<br>
<br>
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-- ========================================<br>
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Justin A. Lemkul<br>
Graduate Research Assistant<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br></div>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<div class="im"><br>
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