[gmx-users] NPT simulation stage

[Ali Alizadeh]

Dear Mahboobe,

I do not know what exactly you mean. You know what, I do not know which
your target system is. I mean when you want to simulate a system you should
know which thermostat

you need. Generally In mailing lists(as I always make some mistake) anyone
knows any details of your system. I do not know where you are(I mean you've
just been familiar with

MD, gromacs ... or not). If you think you need to start and know more about
the condition of simulation, I suggest you selecting one paper and then
reproducing its results.

In that condition, you can be sure of your mistakes or accuracy of your
simulations. Any body can not assign that you must perform a you say 100 ns
for converging.

I suggest you this method as it benefited me.


On Mon, Apr 28, 2014 at 1:15 PM, Mahboobeh Eslami <
mahboobeh.eslami at yahoo.com> wrote:

>
> dear Mr.alizadeh
> thanks for your reply
> the repeatability of average pressure is my problem. average pressure
> isn't  repeatability
>
> when i repeat NPT simulation stage many times, simulation results are very
> different for the pressure average.
> my system is protein-ligand complex. How long do you think is enough for
> the NPT stage?
> Regards
>   On , Mahboobeh Eslami <mahboobeh.eslami at yahoo.com> wrote:
>  dear Mr.alizadeh
> thanks for your reply
> my problem hasn't good repeatability.
> when i repeat NPT simulation stage many times, simulation results are very
> different for the pressure average.
> my system is protein-ligand complex. How long do you think is enough for
> the NPT stage?
> Regards
>
>   On Monday, April 28, 2014 12:48 PM, Ali Alizadeh <
> ali.alizadehmojarad at gmail.com> wrote:
>  Dear Mahboobeh,
>
> I do not know what component your system includes. However, based on my
> experiences, the fluctuation of pressure is high especially for small and
> incompressible systems. Besides, you should increase your simulation time.
> You should not expect that the pressure can converge exactly to the
> pressure you want. I think(I do not know details of your simulations)
> pressure fluctuation is natural, of course not for short simulations, the
> average pressure for equilibriated systems is important.
>
>
>
> ----------------------
> dear justin
> Thank you for your reply.
> My system is about 123,000 atoms and my box is cubic.
> I'm following conditions apply:
>
> pcoupl?????????? = Parrinello-Rahman?????
> Pcoupltype?????? = Isotropic??????????
>
> tau_p??????????? = 0.5???????????????
> compressibility? = 4.5e-5??????????????
> ref_p??????????? = 1.0???????????????
> refcoord_scaling = com
>
> But the average pressure is not good repeatability.
>
> To fix this problem I did two NPT simulation stageThe first 100ps by
> brendsand barostat then 100ps by Parrinello-Rahman barostatbut Still not
> good repeatability. I frequently change tau_p? but I did not get any
> results. Increase the NPT simulation time did not solve the problem.
> I strongly need your help
> Thank you sincerely for your kindness
> On Friday, April 25, 2014 5:08 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
>
>
> On 4/25/14, 2:36 AM, Mahboobeh Eslami wrote:
> > hi GMX users
> > please help me
> > i want to simulate protein-ligand complex by gromacs4.6.5
> > when i repeat NPT simulation stage? many times,? simulation results are
> very different for the pressure average.I sincerely thank you for your
> guidance
> >
>
> Pressure is probably the most ill-defined quantity in MD simulations.? It
> can
> fluctuate dramatically.? Without the actual numbers, it's hard to comment,
> but
> issues related to pressure have been discussed extensively over the list
> in the
> past and there is useful information in
> http://www.gromacs.org/Documentation/Terminology/Pressure.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> --
> Sincerely
>
> Ali Alizadeh
>
>
>
>
>
>


-- 
Sincerely

Ali Alizadeh