[gmx-users] a question related to gmx energy minimization

[Brett]

Dear Tsjerk,
 
Will you please explain to me why the RMSD in this step is so large? For this reason I think there is something wrong.
 
I am looking forward to getting a reply from you.
 
Brett








At 2015-04-26 20:59:59, "Tsjerk Wassenaar" <tsjerkw at gmail.com> wrote:
>Hi Brett,
>
>Too high for what?
>
>You do EM because you just built (part of) your system, and in doing so
>introduced clashes and non-ideal geometries. These lead to high potential
>energy, so you relax them with EM. What you see is how much the system
>relaxed. Noone usually cares how much potential energy was lost during EM.
>The thing that matters is whether the resulting system is relaxed enough to
>run the simulation.
>
>Cheers,
>
>Tsjerk
>
>On Sun, Apr 26, 2015 at 2:43 PM, Brett <brettliu123 at 163.com> wrote:
>
>> Dear All,
>>
>> I just run the command gmx energy -f em.edr -o potential.xvg for my energy
>> minimization step MD, but I find the RMSD given by this command is 142611,
>> which I regard to be too high.
>>
>> Will you please explain to me what leads to the so high RMSD (Err.Est is
>> 53000, Tot-Drift is -341107 KJ/mol)?
>>
>> I am looking forward to getting your reply.
>>
>> Brett
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>
>
>
>-- 
>Tsjerk A. Wassenaar, Ph.D.
>-- 
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