Re: [AMBER] rMD || Distance-Restrained Molecular Dynamics Refinement in Explicit Solvent (AMBER) -- SCRIPT

From: Carlos Simmerling <>
Date: Mon, 2 Nov 2015 07:38:37 -0500

the vlimit error is not "volume" limit, but velocity. it means there is
probably a mismatch in your input structure and the restraints. I'm not
sure that someone can just provide an input, because it would depend on the
source of your restraints, how they are set up, your input coordinates and
so on. someone may have an automated input for this, but if not and you
want to find out what's going wrong, send more info to the list with
details about how you did the setup and what the first step of minimization
tells you. we'd need to see the energy at step 0 or step 1, no later. if
you haven't already carefully looked at this yourself, please do that-
sander gives you a lot of info that can be helpful in understanding what is
going on. you are the best person to figure out what that means, since
others probably do not know all of the steps that you already did, and the
details of the molecule you are simulating.

On Mon, Nov 2, 2015 at 7:29 AM, V. Kumar <> wrote:

> Dear AMBER users
> Could request I request scripts for rMD |or| Distance-Restrained Molecular
> Dynamics Refinement in Explicit Solvent for AMBER 12 with AMBERTOOL-13. I
> have used one from the internet but it led to volume limit errorr with
> vlimit=10, I have changed to vlimti=20, still for few steps it cross like
> 200. So I have tried to perform rMD at in the range 25-30°C still I gor the
> same error. I would highly appreciate if some give me correct scripts.
> thanks
> Vince
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Received on Mon Nov 02 2015 - 05:00:04 PST
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