[gmx-users] com motion
David van der Spoel
spoel at xray.bmc.uu.se
Wed Apr 9 10:52:01 CEST 2003
On Tue, 2003-04-08 at 11:17, Mustafa Toprakçý wrote:
> 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:
It seems that the mdp is correct. The only question then is what is the
- Is the tmeperature of the ligand correct?
> 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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Dr. David van der Spoel, Dept. of Cell & Mol. Biology
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://xray.bmc.uu.se/~spoel
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