[gmx-users] pressure coupling

[mohammad agha]

Thank you very much.

Yes, I checked NPT run and I saw the size and volume of box had been increased. So I increased size of box to 12.
My system consists of: 151 lipids+151 ions+16200 water and antifreezawater molecules

May I know your idea about this, please?

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 10:22 AM
Subject: Re: [gmx-users] pressure coupling
 

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
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>________________________________
> 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.  
>>
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>>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
>>
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>>
>>
>>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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