Re: [gmx-users] temperature shooting up
Dear Mark,Thanks for your help. Actually I did separate runs for flexible and rigid models, and didn't use the equilibrated flexible structure to start with rigid model calculations. But the starting configurations are the same. So do you mean I need to reduce the T-coupling time? If the initial water geometry is not the same as the rigid model, does the program will "enforce" that geometry for water molecules, or to "relax" water molecure towards it? Many thanks,CherryMark Abraham [EMAIL PROTECTED] wrote: Cherry Y. Yates wrote: Dear Mark, Thanks for your help, I followed you instruction, and I can get stable temperature after I remove the temperature coupling. In this case I used the flexible spc itp file. However if I use a rigid spc.itp, after remveing the temperature coupling, the system temperature is shooting up from 300K to thousands degree, the total energy is going up also instead of fluctuating. I attached both the itp files and grompp.mdp files. Let me know what could be wrong. It is really wired to me.The change in the model physics from flexible to rigid is severe one - almost all of the water molecules won't fit the rigid geometry, and will thus be in a high-potential-energy state. If the constraint-enforcing algorithm conserves energy, then that potential energy has to be converted to kinetic energy. Then if the simulation lacks temperature coupling, it is at constant energy and the temperature will be necessarily high. Actually you say you observe rising energy - this is probably because your timestep is too large to conserve energy at this very high temperature (and thus atomic velocity).So the take-home lesson is not to do two perturbations of your model physics at one time. If you really want to start with a flexible water model with temperature regulation and end up with rigid water model at without temperature regulation, do the water transition with temperature coupling still on to give the energy somewhere to flow - to the external bath. I expect you'd need a short temperature coupling constant to make this work in practice. Once that's stable, *now* try taking off temperature coupling.This suggests the question, why you'd want to do this flexible-rigid transition in an equilibration? It would be simpler to start in the rigid domain, and to do energy minimization to correct any geometries before starting MD simulations.Mark___gmx-users mailing listgmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease 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/mailing_lists/users.php __Do You Yahoo!?Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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/mailing_lists/users.php
Re: [gmx-users] temperature shooting up
Cherry Y. Yates wrote: Dear Mark, Thanks for your help. Actually I did separate runs for flexible and rigid models, and didn't use the equilibrated flexible structure to start with rigid model calculations. But the starting configurations are the same. Oh OK - but the same kind of problem can arise if your starting configuration doesn't match the constraints of the rigid model. So do you mean I need to reduce the T-coupling time? See section 3.4.5 of the manual. The smaller the T-coupling time, the harder the T-coupling constraint is. If the initial water geometry is not the same as the rigid model, does the program will enforce that geometry for water molecules, or to relax water molecure towards it? As I said last time, It would be simpler ... to do energy minimization to correct any geometries before starting MD simulations. I've never needed to do this, so can't help with details, but it may be necessary for this EM to use a solvent molecule .itp that has real bonded functions rather than constraints. Thus this EM is actually doing the geometry correction, and the geometry constraint algorithms for MD will work as you'd hope. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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/mailing_lists/users.php
Re: [gmx-users] temperature shooting up
Cherry Y. Yates wrote: Dear Mark, Thanks for your help, I followed you instruction, and I can get stable temperature after I remove the temperature coupling. In this case I used the flexible spc itp file. However if I use a rigid spc.itp, after remveing the temperature coupling, the system temperature is shooting up from 300K to thousands degree, the total energy is going up also instead of fluctuating. I attached both the itp files and grompp.mdp files. Let me know what could be wrong. It is really wired to me. The change in the model physics from flexible to rigid is severe one - almost all of the water molecules won't fit the rigid geometry, and will thus be in a high-potential-energy state. If the constraint-enforcing algorithm conserves energy, then that potential energy has to be converted to kinetic energy. Then if the simulation lacks temperature coupling, it is at constant energy and the temperature will be necessarily high. Actually you say you observe rising energy - this is probably because your timestep is too large to conserve energy at this very high temperature (and thus atomic velocity). So the take-home lesson is not to do two perturbations of your model physics at one time. If you really want to start with a flexible water model with temperature regulation and end up with rigid water model at without temperature regulation, do the water transition with temperature coupling still on to give the energy somewhere to flow - to the external bath. I expect you'd need a short temperature coupling constant to make this work in practice. Once that's stable, *now* try taking off temperature coupling. This suggests the question, why you'd want to do this flexible-rigid transition in an equilibration? It would be simpler to start in the rigid domain, and to do energy minimization to correct any geometries before starting MD simulations. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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/mailing_lists/users.php
