Thank Apoorv and David, If the GMX can use the volecities of y-axis and z-axis, it will overcome this question.
However, it seems that the question was not resolved on the basis of David. Any other people give some advice? Thanks very much. 2011/4/23 David van der Spoel <[email protected]> > On 2011-04-23 09.38, Apoorv Kalyankar wrote: > >> In GROMACS, I believe that whenever an external force is applied, the >> mean velocity of the group is subtracted before rescaling the >> velocities and then the mean velocity is added back in. So if you are >> expecting a plug like flow then there should not be any problem. In >> other cases also, it should not create a problem since your external >> electric field is not that large. >> >> This is correct for the acceleration option, but not for the electric > field. Hence the E-field will introduce friction that will heat up the > system. > > > And yes you should not remove the center of mass motion of the >> molecules otherwise you will get zero velocity. >> > Correct. > > >> Apoorv >> >> On Fri, Apr 22, 2011 at 2:09 AM, lammps lammps<[email protected]> >> wrote: >> >>> Hi, >>> >>> I want to use the option of E_x = 1 0.01 0 to add an electric field to >>> the simulated system in NVT ensemble. >>> >>> Because there should exist an no zero velocity of center-of-mass in the x >>> direction. It seems that it is wrong to directly use the nose-hoover to >>> control the temperature. >>> >>> it is also not reasonable to use nstcomm = 1, because the velocity of >>> center-of mass in the x-axis should be kept when runing. >>> >>> So, How to control the temperature? When calcating the temperature in the >>> process of simulations, how to exclude the velocity of center-of-mass of >>> x >>> direction for controling the right T? >>> >>> Thanks in advance. >>> >>> -- >>> wade >>> >>> -- >>> gmx-users mailing list [email protected] >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>> Please don't post (un)subscribe requests to the list. Use the >>> www interface or send it to [email protected]. >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> > > -- > David van der Spoel, Ph.D., Professor of Biology > Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. > [email protected] http://folding.bmc.uu.se > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- wade
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