AMBER Archive (2008)

Subject: Re: AMBER: VMD Movie 3

From: Ibrahim Moustafa (I.moustafa_at_psu.edu)
Date: Thu May 29 2008 - 16:03:16 CDT

Hi Pat,

   Check your trajectory in ptraj just ³trajin trajectory file²

 If the file is OK, then ptraj will report a successful load of all frames.
If you have a problem, then the trajectory is corrupted and you¹ll know.

 HTH,
 Ibrahim

On 5/29/08 2:47 PM, "Ross Walker" <ross_at_rosswalker.co.uk> wrote:

> Hi Pat,
>
> You should have ended up with 1000 frames in your mdcrd file. I suspect
> therefore that it is corrupt in some way. When you load it into VMD take a
> look in VMD's console window and see if there are any error messages printed.
> You may also want to run it through ptraj (calc an RMSD say) and see if ptraj
> complains that it is corrupted.
>
> All the best
> Ross
>
>
> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
> Campbell, Patrick
> Sent: Thursday, May 29, 2008 11:12 AM
> To: amber_at_scripps.edu
> Subject: AMBER: VMD Movie 3
>
>
> Hello Dr. Simmerling,
>
>
>
>
>
> The ntwx value was 5000 and the nstlim value was 5000000. The job did run to
> completion ie, the nstlim value was reached. I have included the script used
> for the MD below. I welcome any suggestions as to possible solutions.
>
>
>
> Thanks again and do have a great day!
>
> Pat
>
>
>
>
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>
>
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>
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>
> nstlim=5000000,
> dt=0.002,
> ntx=5,
> irest=1,
> ntpr=500,
> ntwr=5000,
> ntwx=5000,
> temp0=300.0,
> ntt=1,
> tautp=2.0,
> ntb=2,
> ntp=1,
> ntc=2,
> ntf=2,
> nrespa=1,
> &end
>

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