[gmx-users] snap shot

[lina]

On Sat, Oct 8, 2011 at 2:21 AM, Nilesh Dhumal <ndhumal at andrew.cmu.edu>wrote:

> Hello,
>
> I have a system with 128 emi (cations) and 128 Cl (anions). I run the
> simulation for 20 ns.
>
> I want to save snap-shot at 5ns, 10ns, 15ns and 20ns.
>
trjconv  use -dt 5000

>
> I don't want to save snap shot for 128 ion-pairs. How can I take average
> over 128 ion pairs and save snap shot for a single ion pair.
>
I don't understand the average mean here?
if you wanna get the average.pdb in some time interval try g_rmsf -ox  -b -e

you may wait for some other better answers.


> Basically I want to use classical md geometry for quatum chemical
> calculation.
>
> I am using Gromacs 4.0.7 version.
>
> Thanks
>
> Nilesh
>
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