AMBER Archive (2009)

Subject: Re: [AMBER] help_me to know the reason

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Sat Apr 18 2009 - 05:53:50 CDT

this should work fine. we don't have enough informatino to help.
please show us the sander script, the mdin file and describe each of
the structures you are using as input. do both target and reference
have exactly the same number of atoms, and are in the same format? how
did you obtain each?

On Sat, Apr 18, 2009 at 12:30 AM, balaji nagarajan
<balaji_sethu_at_hotmail.com> wrote:
>
> Dear AMBER ,
>
> I have posted this problem already ,
> but this time I have a problem in writing the out put files .
>
> I am trying to run the Targeted molecular dynamics  in explicit water ,
>
> The both Targeted and the Reference structure are having same number of molecules (both solute and solvent )
>
> I have given a run in vaccum , The simulation runs ,
>
> After adding water (TIP3P) , I have minimized and equillibriated the system and gave a MD run for 100Ps ,
>
> after that I took both the structures and tried to perform Targeted Molecular dynamics ,
> when I impose the periodic boundary condition ,
> NTB = 2 ,
>
> the sander is utillising 100% CPU and the out put files are empty ,
> and the .mdcrd , vel , mdinfo , rst nothing is being created
>
> But when I do the same with the
> option NTB =0 ,  it prints the outputs , mdcrd , vel , eng , and all
>
> I would like to know is there any technical problem i am facing
> or PBC condition can not be applied for Targeted moleculardynamics
>
>
>
> thanks in advance
> balaji
> UOM
>
>
>
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