AMBER Archive (2008)

Subject: RE: AMBER: vlimit exceeded

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Sat Aug 30 2008 - 13:41:02 CDT

Hi Wang,

> I'm running a 30,000 atoms system in vacuo and get the error
> messages as below:
>
> vlimit exceeded for step 21771; vmax = 20.9636
>
> my .in file is as below:
>
> cell_NPT: 100ps MD
> &cntrl
> imin = 0, irest = 1, ntx = 7,
> ntb = 0,
> cut = 12, ntr=1,
> ntc = 2, ntf = 2,
> tempi = 300.0, temp0 = 300.0,
> ntt = 3, gamma_ln = 2.0,
> nstlim = 50000, dt = 0.001,
> ntpr = 1000, ntwx = 1000, ntwr = 1000
> /
> keep restraints
> 100.0
> RES 217 954
> END
> keep out
> 10.0
> RES 955 1692
> END
> END
>
> could you tell me how to fix it? It will be appreciated greatly!

100.0 is probably too large of a restraint to be using for MD and could be
partly responsible for the problems you are seeing. Although more likely I
suspect it is because you are running without periodic boundaries (ntb=0)
and you are not using Generalized Born here (igb=0) hence this is a gas
phase simulation and your protein probably just isn't stable in a vacuum.
See the first tutorial on the AMBER website for an example + explanation of
this.
 
> And my second question is:
> If I get the message as below
> | RE_POSITION Moving by 0.063118 -3.392424 -0.241462
>
> how can I align the .rst and .mdcrd files to let the center come
> back to the oringinal position? Thanks a lot!!

I'm not sure exactly what you mean here. Do you mean you want to keep the
origin fixed during the simulation? If so I'm not entirely sure how one can
do this, with periodic boundaries you can do it by using center in ptraj to
center the coordinates on say your protein, but without periodic boundaries
I think you might need to write a script to go through the output and add
the RE_POSITION changes to the mdcrd file each time it comes up. You could
also set nscm=0 to force sander to not make the shift but in gas phase you
will eventually end up with your system diffusing a long way from the
origin. Maybe others can comment some more here.

All the best
Ross

/\
\/
|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu