AMBER Archive (2007)

Subject: Re: AMBER: Simulation continuation problem. Cant read restart file!!!!!!

From: Harianto Tjong (harianto_at_mailer.sb.fsu.edu)
Date: Wed Sep 26 2007 - 11:23:14 CDT

Hi,
Your coordinates written on restart file were out of fields. You may use
wrapping in periodic box by setting on iwrap, that means you need to repeat
with the last successful restart file.
This problems have been around & posted serveral times. You could see one of
them from the link:
http://structbio.vanderbilt.edu/archives/amber-archive/2007/1398.php

Regards,
Harianto.

On 9/26/07, Anthony Cruz <acb15885_at_uprm.edu> wrote:
>
> Hi User:
> I have been wotking with a simulation of a heme protein in water. I
> decide to
> run the simulation in multiple steeps of 500 ps. Right now I have 116
> part
> of 500ps (aprox. 60 ns). The problem is that when I re-start the
> simulation
> to do other 5ns of simulation the simulation stop because one of the parts
> cant read the box or the restart file from the previous part. When I check
> the file I found the some of the coordinate were written as *. I restart
> all
> the parts again and have the same problem again. How I can resolve the
> problem of the coordinates in the restart file???
>
> Best regards,
> Anthony
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> 

-- 

http://people.scs.fsu.edu/~harianto

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu