AMBER Archive (2009)

Subject: Re: [AMBER] density and volume in NVT ensamble

From: Adrian Roitberg (roitberg_at_qtp.ufl.edu)
Date: Fri Feb 06 2009 - 08:31:24 CST

Oguz,
Did you look at the equi.out file youself ?
As carlos mentioned, ntb=1 and you have no volume changes.
Indeed, the output file has a pressure of ZERO and no volume/density
data at all.

This is a useful lesson:

Do not say 'both density and volume increase at the end of the md'
simply because you ran a script that it is supposed to give you density
and volume !

If you run a script with the wrong output file, you will get the wrong
data out.

GIGO = Garbage in, Garbage out.

a.

oguz gurbulak wrote:
> I did what you said , but again I saw the same result ( both density and
> volume increase at the end of the md ) . I attached the equ.out to the mail.
>
>
> Thank you very much for your attention.
>
> Kind regards.
>
> 2009/2/16 oguz gurbulak <gurbulakoguz_at_gmail.com>
>
>> I did what you said , but again I saw the same result ( both density and
>> volume increase at the end of the md ) . I attached the equ.out to the mail.
>>
>>
>> Thank you very much for your attention.
>>
>> Kind regards.
>>
>> 2009/2/16 Carlos Simmerling <carlos.simmerling_at_gmail.com>
>>
>> your density and volume plots look the same.
>>> you should not see volume changes with ntb=1. it's impossible to tell
>>> if the problem is in your plots, your data extraction from the mdout,
>>> or sander. maybe you could copy and paste the relevant output directly
>>> from sander? paste in the average and rms sections from the end of the
>>> run. also tell us exactly how you got these values for plotting.
>>>
>>>
>>>
>>> On Mon, Feb 16, 2009 at 8:58 AM, oguz gurbulak <gurbulakoguz_at_gmail.com>
>>> wrote:
>>>> Dear All,
>>>>
>>>> I run a md in NVT ensamble. And I wanted to see the graphs of density
>>> and
>>>> volume with using xmgrace. I realized that both density and volume
>>> increase
>>>> at the end of the md. I didn't find what the problem is about my
>>> operation.
>>>> Could you help me to learn the reason ?
>>>>
>>>>
>>>> MD equilibration
>>>> &cntrl
>>>> imin=0, irest=0, nstlim=10000, dt=0.002, ntx=1,
>>>> ntc=2, ntf=2, ntpr=500, ntwx=500, ntwr=500, ntwe=500, ntwv=500,
>>>> cut=9.825, ntb=1, ntp=0, ntr=0, ntt=1,tautp=2.0, vlimit=5,
>>>> tempi=0.0, temp0=273.0,
>>>> /
>>>>
>>>>
>>>> Thank you very much for your attention.
>>>>
>>>> Kind regards.
>>>>
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>>
>>
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-- 
                            Dr. Adrian E. Roitberg
                              Associate Professor
                             Quantum Theory Project
                            Department of Chemistry

                  Senior Editor. Journal of Physical Chemistry
                           American Chemical Society

University of Florida                         PHONE 352 392-6972
P.O. Box 118435                               FAX   352 392-8722
Gainesville, FL 32611-8435                    Email adrian_at_qtp.ufl.edu

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