On 17/12/2011 5:40 PM, mohammad agha wrote:
Thank you very much.
Excuse me, I did another thing, may I know is it right, Please?
I did editconf before equilibration (pr.mdp) and increased my box
vector from 11.2 to 12:
editconf -f em3.gro -o out.gro -c -d 1.0 -bt cubic -box 12 12 12
-center 6 6 6
and I minimized my system (out.gro) and then did equilibration
(pr.mdp). My system gave me warning for box sizes 11.4, 11.6 and 11.8,
consequently I select 12 and pr.mdp is run without warning.
Is it right?
We don't know. You've been changing your box volume but haven't said
anything about the contents. You need to look at how the box changes
over the NPT run, like I said last time. If your generated solvent
density was wrong such that you needed to add about 20% more volume,
then expect to need to equilibrate for quite a while.
Mark
Best Regards
Sara
------------------------------------------------------------------------
*From:* Mark Abraham <mark.abra...@anu.edu.au>
*To:* Discussion list for GROMACS users <gmx-users@gromacs.org>
*Sent:* Saturday, December 17, 2011 9:31 AM
*Subject:* Re: [gmx-users] pressure coupling
On 17/12/2011 4:58 PM, mohammad agha wrote:
Dear GROMACS Users
I have a warning after doing pr.mdp as followed, I read errors in
GROMACS site and checked mailing list, but my warning is only step1
and after that equilibration is run normally till end.
5000000 steps, 150000.0 ps.
step 0
Step 1 Warning: pressure scaling more than 1%, mu: 1.04679 1.04679
1.04679
Step 1 Warning: pressure scaling more than 1%, mu: 1.04679 1.04679
1.04679
my pr.mdp about pressure coupling is:
pcoupl = berendsen
pcoupltype = isotropic ; uniform scaling of box vectors
tau_p = 4 ; time constant, in ps
ref_p = 1.0 ; reference pressure, in bar
compressibility = 4.5e-5 ;isothermal compressibility of water, bar^-1
I work in Martini Coarse-Grained and my time step is 0.03 ps. I
increased tau_p but my warning increased to step 1 and step 11, I
think this warning since it is only in initial steps isn't important,
is my idea right?
That kind of thing is normal in the very early stages of NPT
equilibration when the volume is not quite right. mdrun is just
warning you that there are some changes going on. Use g_energy to see
those. If it bothers you, then you will want to adjust your density
(i.e. number of water molecules) before starting.
Mark
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