[gmx-users] Re: grommp_md error

Vitaly Chaban vvchaban at gmail.com
Tue Jul 13 07:22:37 CEST 2010


I think you make the things more complicated than they really are.

> 2- I have a question about doing NPT for compressing the system. Can I also
> do NVT for a short time and when the chain has a more realistic structure ,
> take that structure and change the volume myself? I am just asking for the
> sake of learning.. This doesnt mean I am not going to do follow your
> advise..

You should compress the system in such a way that it becomes a bit
smaller than you need. Then one can "enlarge" the system in the GRO
file (or using editconf) if needed. For running such MD runs, you
should use your complete system, not the elementary cell, certainly.

As for me, I think you do not need NVT at all.

> 3- Also If I want to find the pressure which gives the size I want, I need
> to wait till the end of simulation to see the volume (eg with g_energy) and
> repeat this to find the desired volume by try and error?

I think you can plot system volume vs pressure using multiple NPT runs.

Dr. Vitaly Chaban

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