[gmx-users] snap shot

[Nilesh Dhumal]

Hello,

How can I save the coordinates  (in pdb or xyz format) for a particular
snap shot.

Nilesh

On Sat, October 8, 2011 10:06 am, lina wrote:
> 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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