AMBER Archive (2007)

Subject: Re: AMBER: Constant volume simulations

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Tue Apr 10 2007 - 10:39:45 CDT

Christopher,

Your system is not expanding ... Its just that the waters move out of
the primary box .... What you see is actually very normal. In order to
see your original box you need to image back to the primary box. Usually
I do that with ptraj postprocessing (see the image and center command in
ptraj) ...

cheers
vlad

P.S. Isn't 10.000 a too large value for ntwx for a 1.000.000 steps
simulation ???

Christopher Gaughan wrote:

> here is my md.in <http://md.in> file:
>
> &cntrl
> imin = 0, nmropt = 0,
>
> ntx = 1, irest = 0, ntrx = 1,
>
> ntxo = 1, ntpr = 10000,
> ntwr = 50,
> ntwx = 10000, ntwv = 0, ntwe = 0,
> ioutfm = 0, ntwprt = 0,
>
> ntf = 2, ntb = 1, dielc = 1.0,
> scnb = 2.0, scee = 1.2
>
> ibelly = 0, ntr = 0,
>
> nstlim = 1000000,
> dt = 0.002, pres0 = 1,
> temp0 = 300.00, tempi = 300.0, ig = 71277,
> ntt = 1,
> tautp = 1.0, vlimit = 0.0, ntp = 0,
>
> ntc = 2, tol = 0.00005,
>
> //
>
> However, I have erred in that the output from amber does not show that
> the volume is increasing (it shows no values for each time point). The
> problem arises when I view my trajectory in VMD 1.8.5- The waters,
> which initially start out as a box around my peptide, appear to to
> just expand out throughout the simulation.
>
> I am not sure if this is just a visualization problem inherent from
> the use of periodic boundary conditions (however I use the periodic
> box option in VMD) or whether the system is indeed expanding.
>
>
>
> On 4/9/07, * David A. Case* <case_at_scripps.edu
> <mailto:case_at_scripps.edu>> wrote:
>
> On Mon, Apr 09, 2007, Christopher Gaughan wrote:
> >
> > I am running simulations in Amber 8 using N V T ensemble.
> However, when I
> > track the volume during the MD runs I notice that it keeps
> increasing
> > throughout the simulation.
>
>
> We need more information. You are obviously not doing a constant
> volume
> simulation. But all you have said so far is what you *intended*
> to do, not
> what you actually did (i.e. not your input). Be sure to check the
> value of
> ntp.
>
>
> .....dac
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu <mailto:amber_at_scripps.edu>
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> <mailto:majordomo_at_scripps.edu>
>
> 

-- 
----------------------------------------------------------------------------
Dr. Vlad Cojocaru

EML Research gGmbH
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg

Tel: ++49-6221-533266
Fax: ++49-6221-533298

e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de

http://projects.villa-bosch.de/mcm/people/cojocaru/

----------------------------------------------------------------------------
EML Research gGmbH
Amtgericht Mannheim / HRB 337446
Managing Partner: Dr. h.c. Klaus Tschira
Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter
http://www.eml-r.org
----------------------------------------------------------------------------

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