[gmx-users] pressure coupling

[Mark Abraham]

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.Abraham at anu.edu.au>
> *To:* Discussion list for GROMACS users <gmx-users at 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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