[gmx-users] com motion

[Mustafa Toprakçý]

Ok David,
The temperature is what I want. According to my understanding the 
update algorithm corrects the VCM and prevents accumulation of kinetic
energy in the center of mass. When I checked the com xvg file this is
clearly seen. Just like the temperature, the com koordinates does not 
change much.
  so it seems the code does not sample such kind of motion efficiently.
Such a simulation may be sampled under external forces but that would
be too unrealistic. Because it would be better to sample under intermolecular forces.

Regards,
Mustafa





 --- On Wed 04/09, 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: 09 Apr 2003 10:51:30 +0200
Subject: Re: [gmx-users] com motion

On Tue, 2003-04-08 at 11:17, Mustafa Toprakçý wrote:<br>> <br>> Hi David,<br>> Yes, this is a complex. In the topology file I have given it as one <br>> molecule under [molecules] header. I have manually placed the ligand<br>> and miniöized it using steep. I made two groups, proteýn and ligand<br>> then heated the temp of the ligand to 1000K while keeping the protein<br>> at 300K. After this I made 400ps. simulation. Here is my mdp file:<br>> <br>It seems that the mdp is correct. The only question then is what is the<br>question? <br>- Is the tmeperature of the ligand correct?<br><br><br><br>> itle           	        =  MD relaxation procedure<br>> cpp             	=  /lib/cpp<br>> integrator      	=  md<br>> dt              	=  0.002 	; ps<br>> nsteps          	=  200000  	; total 400 ps.<br>> nstxout         	=  500   	; in steps<br>> nstvout         	=  500   	; in steps<br>> nstfout         	=  1000  	; in steps<br>> nstlog          	=  100   	; in steps<br>> nstenergy   
     	=  100   	; in steps<br>> nstlist         	=  10    	; in steps<br>> ns_type         	=  grid<br>> vdwtype                 =  cut-off<br>> coulombtype             =  cut-off<br>> rlist           	=  1.6   	; nm<br>> rcoulomb        	=  1.6   	; nm<br>> rvdw            	=  1.6   	; nm<br>> nstcomm 		=  0 	        ; should be used with vacuum.<br>> ; Center of Mass motion group is not defined.<br>> comm_mode       	=  none<br>> ; freeze groups<br>> freezegrps              =  protein<br>> freezedim               =  Y Y Y<br>> ; Temperature coupling in groups are defined.<br>> Tcoupl          	=  berendsen<br>> tc_grps         	=  protein  ligand<br>> tau_t           	=  0.01     0.03<br>> ref_t           	=  300      1000<br>> ; Groups to write to energy file.<br>> energygrps      	=<br>> energygrp_excl		=<br>> ; Generate velocities only neded for the first cycle.<br>> gen_vel         	=  no<br>> gen_temp        	=  1000<br>> gen_seed        	=  173529 	; arbitrary<br>> <b
 r>> <br>> Mustafa<br>> <br>> <br>> <br>>  --- On Tue 04/08, David van der Spoel < spoel at xray.bmc.uu.se > wrote:<br>> From: David van der Spoel [mailto: spoel at xray.bmc.uu.se]<br>> To: gmx-users at gromacs.org<br>> Date: 08 Apr 2003 10:51:12 +0200<br>> Subject: Re: [gmx-users] com motion<br>> <br>> 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<br>>  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/mail
 man/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><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/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>> <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>++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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