Re: AMBER: TIP5P water simulation using AMBER7

From: Adrian Roitberg <>
Date: Sun, 11 Nov 2007 11:29:11 -0500

I agree with carlos that there are too many flags in your file that
either do nothing, or their default would be just fine.

One wild guess, try adding iwrap=1 to your input file. This puts the
molecules back inside the central box when writing.

That would certainly help with the restart and crd file that have finite
precision. When the system 'dies', you can then go back to your restart
file and maybe get a hint of what happened.

It should not, however, help with your problem WHILE running, which is
unrelated to iwrap.


Biman Jana wrote:
> Yes, this is just a bulk simulation of TIP5P in NPT condition, nothing
> else. please let me know your valuable suggestions where i am going wrong.
> On Sat, 10 Nov 2007, Carlos Simmerling wrote:
>> this is just TIP5P and nothing else?
>> On Nov 10, 2007 9:57 AM, Biman Jana <> wrote:
>>> Hi,
>>> I want to do TIP5P water simulation in NPT ensamble. After
>>> equlibrating
>>> the system in the desied temperature using NVT ensamble i am swithing to
>>> NPT simulation. After some steps ( ~ 1500000) i am getting the error
>>> message like " For step number 1500000 vlimit exceeded" and the
>>> program is
>>> getting stuck giving all the coordinate and velocity in the restart file
>>> NAN. Please suggest me something. Below i am attaching the Simulation
>>> controll file for NPT simulation i am using now.
>>> Here is the file
>>> &cntrl
>>> IREST=1, IMIN=0, NMROPT=0, NTPR=100,
>>> NTX=7, IG=71277, TEMPI=290, HEAT=5.0,
>>> NTB=2, NTC=2, TOL=0.000001, NTF=2, NSNB=25,
>>> NTT=1, TEMP0=290.0, DTEMP=5.0, TAUTP=0.5,
>>> NTP=1, PRES0=1.0, COMP=44.6,TAUP=1.0,
>>> NSTLIM=200000, T=0.0, DT=0.002,
>>> CUT=8.0, SCNB=2.0, SCEE=1.2, DIELC=1.0,
>>> DX0=0.01, DXM=0.5,
>>> IBELLY=0, NTWX=0, NSCM = 1000,NTWR=500
>>> &end
>>> &ewald
>>> SKINNB=1.5,
>>> &end
>>> &wt
>>> TYPE='TEMP0',ISTEP1=1,ISTEP2=200000,VALUE1=290.0,VALUE2=290.0,
>>> &end
>>> &wt TYPE='END'
>>> &end END
>>> Suggestions will be highly appreciated.
>>> Biman Jana
>>> --
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                            Dr. Adrian E. Roitberg
                              Associate Professor
               Quantum Theory Project and Department of Chemistry
University of Florida                         PHONE 352 392-6972
P.O. Box 118435                               FAX   352 392-8722
Gainesville, FL 32611-8435                    Email
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Received on Wed Nov 14 2007 - 06:07:13 PST
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