[gmx-users] 答复： position restraint during NVT equllibration

[Justin Lemkul]

On 2/19/14, 8:57 AM, sunyeping wrote:
>
>
> ------------------------------------------------------------------
> 发件人：Justin Lemkul <jalemkul at vt.edu>
> 发送时间：2014年2月19日(星期三) 21:35
> 收件人：gromacs <gmx-users at gromacs.org>; 孙业平 <sunyeping at aliyun.com>
> 主　题：Re: [gmx-users] position restraint during NVT equllibration
>
>
>
> On 2/19/14, 4:20 AM, sunyeping wrote:
>  >
>  > Dear all,I am doing MD simulation on a protien which has three chains. It
> needs position restrain when doing NVT equillibration. When do MD simulation on
> a protein having only one chains, pdb2gmx will generation a posre.itp file. By
> including
>  > ; Include Position restraint file
>  > #ifdef POSRES
>  > #include "posre.itp"
>  > #endif
>  >
>  > in topol.top file and including
>  >
>  > define = -DPOSRES
>  >
>  > in the NVT.mdp file
>  >
>  > the position restrain on potein can be realized. However, if the protein has
> three chains, pdb2gmx generates not a posre.itp file but three itp files (
> posre_Protein_chain_A.itp, posre_Protein_chain_B.itp,
> posre_Protein_chain_C.itp). Under such circumstance, how should we do position
> restaint on potein?
>
> Have you looked at the topology? You'll find a strikingly similar control
> structure for each of the chains.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================t
> The topology is as following:
> ;
> ;File 'topol.top' was generated
> ;By user: root (0)
> ;On host: localhost.localdomain
> ;At date: Wed Feb 19 09:58:58 2014
> ;
> ;This is a standalone topology file
> ;
> ;It was generated using program:
> ;pdb2gmx - VERSION 5.0-dev
> ;
> ;Command line was:
> ;pdb2gmx -f KI-10_JKL.pdb -ignh -o complex.gro
> ;
> ;Force field was read from the standard Gromacs share directory.
> ;
>
> ; Include forcefield parameters
> #include "gromos43a1.ff/forcefield.itp"
>
> ; Include chain topologies
> #include "topol_Protein_chain_J.itp"
> #include "topol_Protein_chain_K.itp"
> #include "topol_Protein_chain_L.itp"
>
> ; Include water topology
> #include "gromos43a1.ff/spce.itp"
>
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ;  i funct       fcx        fcy        fcz
>     1    1       1000       1000       1000
> #endif
>
> ; Include topology for ions
> #include "gromos43a1.ff/ions.itp"
>
> [ system ]
> ; Name
> Protein in water
>
> [ molecules ]
> ; Compound        #mols
> Protein_chain_J     1
> Protein_chain_K     1
> Protein_chain_L     1
> SOL         19193
> NA               64
> CL               58
>
>
>   What do you mean when you talking about "strikingly similar control structure
> for each of the chains"?

Open each of the chain topologies in a text editor.  They will have the same 
#ifdef blocks that you are used to seeing in a single protein .top file.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================