[gmx-users] How to control the temperature when using an electric field?
lammp2forum at gmail.com
Sat Apr 23 10:43:55 CEST 2011
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 <spoel at xray.bmc.uu.se>
> 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
> And yes you should not remove the center of mass motion of the
>> molecules otherwise you will get zero velocity.
>> On Fri, Apr 22, 2011 at 2:09 AM, lammps lammps<lammp2forum at gmail.com>
>>> 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
>>> direction for controling the right T?
>>> Thanks in advance.
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> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
> spoel at xray.bmc.uu.se http://folding.bmc.uu.se
> gmx-users mailing list gmx-users at gromacs.org
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