Re: [AMBER] vlimit exceeded after 10ns MD

From: Bill Ross <ross.cgl.ucsf.EDU>
Date: Mon, 26 Jul 2010 17:21:02 -0700

> ntt=3, ...

For what it's worth, I came across this from 2007, not sure
if it still applies:

  http://structbio.vanderbilt.edu/archives/amber-archive/2007/1141.php

> On the other hand, Langevin (ntt=3) simulations can also exhibit funny
> behavior, especially if the same random number seed is used for repeated
> simulations. This problem has a long history, but a good recent
> overview is
> here:
>
> %A B.P. Uberuaga
> %A M. Anghel
> %A A.F. Voter
> %T Synchronization of trajectories in canonical molecular-dynamics
> simulations: Observation, explanation, and exploitation %J J. Chem.
> Phys.
> %V 120
> %P 6363-6374
> %D 2004
>
> A recommendation is that you should explicitly set the random number
> seed
> ("ig") to new values at each restart of an ntt=3 simulation. 

---
> I am doing an MD simulation study of my protein+water system.
> I minimized the whole system (all heavy atoms + backbone atoms + CA atoms
> restrained) first and then proceeded for the trajectory production.
> However, after 10 ns of trajectory production, I couldn't move further. The
> mdout file shows that "vlilmit exceeded for step 0; vmax =  1132.4370"
> I checked the mailing list and found the information regarding the vlimit
> problem during the Minimization steps, but here I am getting in the
> production phase.
> Can you please suggest me looking to my input file, that where I am going
> wrong.
>  Production phase molecular dynamics run
>  &cntrl
> imin=0, irest=1, ntx=5,
> ntt=3, tempi=300.0, temp0=300.0, gamma_ln=5.0, nrespa=1,
> ntp=1, taup=2.0,
> ntb=2, ntc=2, ntf=2,
> nstlim=1000000, cut=8.0,
> ntwe=1000, ntwx=1000, ntpr=500,
>  /
> eof
> I am using the AMBER-9 version.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jul 26 2010 - 17:30:02 PDT
Custom Search