AMBER Archive (2006)

Subject: Re: AMBER: Restart problem on PMEMD with position restraint.

From: Robert Duke (rduke_at_email.unc.edu)
Date: Mon Sep 18 2006 - 13:20:27 CDT

Chunhu -
Seems likely to me this is a simulation protocol problem, not a
pmemd-specific problem. I will leave it to others to elaborate on how to
get through the various minimizations, NVT and NPT runs, with a temp rampup
from 0 to 300 in there somewhere (I remember folks are now using ntt 3 to
simplify this; I still do things the old-fashioned way myself). Perhaps
looking at the tutorials might help some? You say this is a protein G
simulation; there is a reference to dna in the second mdin that I presume is
a failure to edit a comment.
Regards - Bob

----- Original Message -----
From: "Chunhu Tan" <tanc_at_uci.edu>
To: <amber_at_scripps.edu>
Sent: Monday, September 18, 2006 1:46 PM
Subject: AMBER: Restart problem on PMEMD with position restraint.

>
> Hi, All,
>
> I got a Vlimit error when I wanted to restart a PMEMD simulation with
> position restraint. My system is protein G solvated in a TIP3P water box
> with 11 angstroms buffer. After the minimization, I first run 20ps NVT
> simulation, then 20ps NPT simulation. All these were OK, but when I
> wanted to restart the NPT simulation, I got the Vlimit error, even I
> used exact the same input file as the first NPT run.
> I am using AMBER9, and here are the inputs:
>
> 1) MD_NVT.IN
> &cntrl
> imin = 0,
> irest = 0, ntx = 1,
> ntb = 1,
> ntt = 3, gamma_ln =1.0,
> iwrap = 1,
> ntf = 2, ntc = 2, tol = 0.000001,
> temp0 = 300, tempi = 300,
> nstlim= 10000,
> ntpr = 1000, ntwr = 1000, ntwx = 10000,
> dt = 0.002,
> cut = 9,
> ntr = 1
> /
> &ewald
> skinnb = 1.
> /
> Hold the protein fixed
> 50.0
> RES 1 56
> END
>
> _______________________________________
> 2) MD_NPT.IN
> &cntrl
> imin = 0,
> irest = 1, ntx = 5,
> ntb = 2, ntp = 1,
> ntt = 1, iwrap = 1,
> ntf = 2, ntc = 2, tol = 0.000001,
> temp0 = 300,
> nstlim= 10000,
> ntpr = 5000, ntwr = 5000, ntwx = 200000,
> dt = 0.002,
> cut = 9,
> ntr = 1
> /
> &ewald
> skinnb = 1.
> /
> Hold the nucleic acid fixed
> 50
> RES 1 56
> END
> END
>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>

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