RE: [AMBER] vlimit exceeded for step

From: Ross Walker <>
Date: Fri, 9 Apr 2010 11:59:53 -0700

Hi Rilei,

> When I set up dt=0.001,  everything goes well. However, when I try
> dt=0.002, some bugs appeared! I even found someone even asked such
> question in the mail-list, but I still found it could not solve my
> problem. Can anyone give me some help?

These are not bugs but rather something telling you there is something wrong
with your simulation.

A few comments on your input file:
>  &cntrl
>   ntx=1,
>   irest=0,
>   imin=0,
>   ntpr=10,
>   ntwx=10,
>   ntwr=50,
>   nstlim=5000,
>   dt=0.002,
>   ntt=3,
>   gamma_ln = 1.0,
>   temp0=300,
>   tempi=300,
>   tautp=1,

tautp is meaningless with ntt=3.

>   igb=0,
>   ntb=0,

You are running a vacuum simulation with no solvent whatsoever. I very much
doubt your system is stable in a vacuum at 300K. A lot of biological
molecules decompose under such conditions. I would suggest running with
either implicit or explicit salvation. Unless you are specifically trying to
reproduce vacuum results.

>   cut=15,

You should NOT use a cut off with non-periodic calculations. Set this to

>   ntr=1,
>   fcap=10.0,

Are you running a solvent cap? If so, why? fcap is only meaningful in this

>   ivcap=0,
>   tol=0.000001,

You set the shake tolerance but nowhere do you turn on shake. Your default
if NTF=1 and NTC=1. This means your hydrogens are free to move. VERY FAST.
Faster than the nyquist limit for a 2fs time step. This is the cause of your
vlimit failures, they are because of integration errors caused by using a
timestep too long for the simulation parameters. Try turning on shake with
NTF=2 and NTC=2.

>   ntr=1, restraint_wt=10.0, restraintmask=':1-90, 93-140, 151-180, 196-
> 234, 242-256, 265-278, 283-310, 322-360, 371-410',
>   &end

A restraint_wt of 10.0 is probably a little big, reduce this to between 1.0
and 5.0. You should also check that you are providing a reasonable reference
structure, and not one that has massively different coordinates to your

All the best

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | |

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Received on Fri Apr 09 2010 - 12:30:05 PDT
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