[gmx-users] com motion

Mustafa Toprakçý denn22 at excite.com
Tue Apr 8 11:18:01 CEST 2003

Hi David,
Yes, this is a complex. In the topology file I have given it as one 
molecule under [molecules] header. I have manually placed the ligand
and miniöized it using steep. I made two groups, proteýn and ligand
then heated the temp of the ligand to 1000K while keeping the protein
at 300K. After this I made 400ps. simulation. Here is my mdp file:

itle           	        =  MD relaxation procedure
cpp             	=  /lib/cpp
integrator      	=  md
dt              	=  0.002 	; ps
nsteps          	=  200000  	; total 400 ps.
nstxout         	=  500   	; in steps
nstvout         	=  500   	; in steps
nstfout         	=  1000  	; in steps
nstlog          	=  100   	; in steps
nstenergy       	=  100   	; in steps
nstlist         	=  10    	; in steps
ns_type         	=  grid
vdwtype                 =  cut-off
coulombtype             =  cut-off
rlist           	=  1.6   	; nm
rcoulomb        	=  1.6   	; nm
rvdw            	=  1.6   	; nm
nstcomm 		=  0 	        ; should be used with vacuum.
; Center of Mass motion group is not defined.
comm_mode       	=  none
; freeze groups
freezegrps              =  protein
freezedim               =  Y Y Y
; Temperature coupling in groups are defined.
Tcoupl          	=  berendsen
tc_grps         	=  protein  ligand
tau_t           	=  0.01     0.03
ref_t           	=  300      1000
; Groups to write to energy file.
energygrps      	=
energygrp_excl		=
; Generate velocities only neded for the first cycle.
gen_vel         	=  no
gen_temp        	=  1000
gen_seed        	=  173529 	; arbitrary


 --- On Tue 04/08, David van der Spoel < spoel at xray.bmc.uu.se > wrote:
From: David van der Spoel [mailto: spoel at xray.bmc.uu.se]
To: gmx-users at gromacs.org
Date: 08 Apr 2003 10:51:12 +0200
Subject: Re: [gmx-users] com motion

On Tue, 2003-04-08 at 10:06, Mustafa Toprakçý wrote:<br>> <br>> Dear gromacs team,<br>> I have recently completed a simulation in which I sampled center of mass motion of the ligand for 400ps. The receptor stayed fixed but <br>> the ligand was free to move. I used,<br>> comm_mode = none <br>> nstcomm   = 0<br>> <br>> When I checked the results, the com of the ligand has made not more than 0.1 nm. in all drections. I used high temperatures and there should be more than that.It seems there is still constraint on the com motion. How can I completely remove this?<br>> <br>please supply more detail. Is this a complex?<br><br>> Thanks<br>> Mustafa<br>> <br>> <br>> <br>> <br>> <br>> <br>> <br>> <br>> _______________________________________________<br>> Join Excite! - http://www.excite.com<br>> The most personalized portal on the Web!<br>> _______________________________________________<br>> gmx-users mailing list<br>> gmx-users at gromacs.org<br>> http://www.gromacs.org/mailman/listinf
 o/gmx-users<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request at gromacs.org.<br>> <br>-- <br>Groeten, David.<br>________________________________________________________________________<br>Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology<br>Husargatan 3, Box 596,  	75124 Uppsala, Sweden<br>phone:	46 18 471 4205		fax: 46 18 511 755<br>spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel<br>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++<br>_______________________________________________<br>gmx-users mailing list<br>gmx-users at gromacs.org<br>http://www.gromacs.org/mailman/listinfo/gmx-users<br>Please don't post (un)subscribe requests to the list. Use the<br>www interface or send it to gmx-users-request at gromacs.org.<br>

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