AMBER Archive (2006)

Subject: Re[2]: AMBER: Input conversion error.

From: Sergey Krishtal (skrishtal_at_mail.ru)
Date: Mon Mar 13 2006 - 08:52:23 CST

Hello!
I performed normal MD simulation at the highest temperature (600 K) during equilibration and the latter was stable. The time step was 1 fs. Now I'm performing normal MD simulations with time step of 0.5 fs to see if this problem still exists.

Best regards,
Sergey

-----Original Message-----
From: Carlos Simmerling <carlos_at_ilion.bio.sunysb.edu>
To: amber_at_scripps.edu
Date: Sat, 11 Mar 2006 14:23:29 -0500
Subject: Re: AMBER: Input conversion error.

>
> if your velocities are too large to fit, then it's a sign that
> the simulation has a problem. Making the format longer
> would not help. You might want to try using a smaller time
> step. Another good test would be to run normal MD
> at the highest temperature you used for REMD and see if
> it is stable.
>
> Sergey Krishtal wrote:
> > Dear Amber users,
> >
> > I'm performing REMD simulations with Amber 8. Some of replicas have temperature greater than 500 K. Sometimes it happens that for such replicas the velocities of atoms are written in the .rst file as ************. As I understand, it is connected with fortran format restrictions used to write velocities into .rst file. Because of having ******** instead of numbers mpi stops the simulations with message as follow:
> >
> > forrtl: severe (64): input conversion error, unit 9
> >
> > By the way, the same problems happened when I equilibrated some of rerlicas at temperatures greater than 500 K with ntt=3. Equilibration with ntt=1 solved that but the problem itself still exists.
> > I tried to change default VLIMIT value but it didn't result in disappearance of *********** in .rst files. Probably I changed VLIMIT not enough (up to 100).
> >
> > Probably, changing fortran format for .rst file will solve the problem but I'm not sure I know all places in the Amber where I should make such changes.
> >
> > I would be grateful for any help.
> >
> > Best regards,
> > Sergey Krishtal
> >
> >
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