[gmx-users] Re: invacuo minimization

[David van der Spoel]

anwar at cdfd.org.in wrote:
> Hi David,
> I have checked the mdout.mdp and as you said it has pbc = xyz. What do 
> I do now. I havent run editconf, but why it is taking pbc conditions? How 
> do I remove these?? 
pbc=no

> thanks
> Anwar
> 
> ----------------------
> Mohd Anwaruddin
> Project Assistant
> C/o DR.H.A.Nagarajaram
> Lab of Computational Biology and Bioinformatics
> Center for DNA Fingerprinting and Diagnostics(CDFD)
> Nacharam
> Hyderabad-500 076
> INDIA.
> Tel: +91-8413-235467,68,69,70 ext 2019
> anwar.m1 at gmail.com
> -----------------------
> 
> 
> 
> ---------REPLY TO-------------
> Date:Thu Sep 07 18:00:08 GMT+08:00 2006
> FROM: gmx-users-request at gromacs.org
> To: gmx-users at gromacs.org
> Subject: gmx-users Digest, Vol 29, Issue 14
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> Today's Topics:
> 
>    1. Re: invacuo minimization (David van der Spoel)
>    2. LIE energy calculation! (Mikko Hellgren)
> 
> 
> ---------------------------------------------------------------------- 
> 
> Message: 1
> Date: Thu, 07 Sep 2006 10:44:52 +0200
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> Subject: Re: [gmx-users] invacuo minimization
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <44FFDC04.4030707 at xray.bmc.uu.se>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> anwar at cdfd.org.in wrote:
>> Dear gmx users,
>> When I am minimizing a trimer protein in vacuum by SD as well as CG methods, 
>> one of the monomer gets apart from the rest of the protein and places 
> itself 
>> away from the other two monomers, which are intact. No periodic box is 
>> assigned. But when I am running editconf and assigning a box, then the 
>> structures are intact. What is the reason for the above behaviour? 
>> I am pasting the em.mdp below:
> 
> chekc your mdout.dmp, the default pbc = xyz
> 
>> cpp                 =  /lib/cpp
>> define              =  -DFLEX_SPC
>> constraints         =  none
>> ;integrator          =  CG
>> integrator          =  steep
>> nsteps              =  1000
>> ;
>> ;       Energy minimizing stuff
>> ;
>> emtol               =  100
>> ;for SD
>> emstep              =  0.1
>> ;for CG
>> ;emstep              =  0.001
>>
>> nstcomm             =  1
>> ns_type             =  grid
>> rlist               =  1
>> rcoulomb            =  1.0
>> rvdw                =  1.0
>> Tcoupl              =  no
>> Pcoupl              =  no
>> gen_vel             =  no
>>
>>
>> Anwar
>>
>> ----------------------
>> Mohd Anwaruddin
>> Project Assistant
>> C/o DR.H.A.Nagarajaram
>> Lab of Computational Biology and Bioinformatics
>> Center for DNA Fingerprinting and Diagnostics(CDFD)
>> Nacharam
>> Hyderabad-500 076
>> INDIA.
>> Tel: +91-8413-235467,68,69,70 ext 2019
>> anwar.m1 at gmail.com
>> -----------------------
>>
>>
>>
>> -
>>
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> 
> 


-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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