Hi Gromacs Friends, Thank you for your reply and nice suggestion. I read the wikipedia article ..http://en.wikipedia.org/wiki/Flying_ice_cubesuggested by Mark..
as per the article.. More conservatively, the rate of velocity rescaling can be reduced, the scale factor computed over a time-averaged sample of instantaneous temperatures, or an alternative means of thermostatting such as the Nosé-Hoover thermostat <http://en.wikipedia.org/wiki/Nos%C3%A9-Hoover_thermostat> can be used. So I used the Nose-Hover thermostat.. after finished mdrun , to see movie I used the command trjconv -s ..tpr -f ...xtc -pbc nojump -o protein.pdb -dt 10 -center I found that after these command also my molecule some time moving the out of box ..Is it right??? In these MD run I not remove COM(center of motion) so I want to check it is not producing any misleading and run is not wrong (No flying ice cube effect)..?? the grommp warning was like .. WARNING 1 [file md.mdp]: You are not using center of mass motion removal (mdp option comm-mode), numerical rounding errors can lead to build up of kinetic energy of the center of mass And I used Maxwarn 1... So Now I want to check is these warning affect my run ...which proparty I have to check ?? Thank you in advance.. On Sat, Mar 24, 2012 at 9:41 PM, Mark Abraham <mark.abra...@anu.edu.au>wrote: > On 24/03/2012 11:06 PM, rama david wrote: > >> Hi Gromacs Specialist, >> I want to study How the protein interact >> with each other ?? >> > > Great, but whether or not you remove center of mass translation *of the > whole system* has nothing directly to do with it. > > > I run one simulation with following MDP file option .. >> comm_mode = Linear ; remove center of mass >> translation >> nstcomm = 1 ; [steps] frequency of >> mass motion removal >> comm_grps = Protein Non-Protein ; group(s) for center of >> mass motion removal >> >> >> Now I decided to remove the center of mass >> with following option ......... >> > > Changing this option to "None" doesn't "remove the center of mass", it > stops removing the motion of the center of mass. > > > comm_mode = None ; remove center of mass >> translation >> nstcomm = ; [steps] frequency of >> mass motion removal >> comm_grps = ; group(s) for center of >> mass motion removal >> >> I got the following warning at the command grompp... >> >> WARNING 1 [file md.mdp]: >> You are not using center of mass motion removal (mdp option comm-mode), >> numerical rounding errors can lead to build up of kinetic energy of the >> center of mass >> >> I run with maxwarn 1 , Is I am right?? >> > > Do you know why you can ignore this warning? If not, do not use -maxwarn. > > > >> What Is reason for above error?? >> > > You're getting a warning because you are doing something that might be > wrong - in fact, likely to be wrong. See http://en.wikipedia.org/wiki/** > Flying_ice_cube <http://en.wikipedia.org/wiki/Flying_ice_cube> > > Mark > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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 gmx-users-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >
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