Re: [gmx-users] Large fluctuation of protein temperature with nose hoover thermostat
OK thank you Omer, for you response The group PROTEIN isn't very large as the group NONPROTEIN, therefore its total kinetic energy fluctuates more. --Omer. On Wed, Sep 16, 2009 at 12:10, Stephane Abel wrote: > tc-grps = Protein Non-Protein ; two coupling groups - more accurate > tau_t = 0.4 0.4 ; time constant, in ps > ref_t = 310 310 ; reference temperature, one for each group, in K Energy Average RMSD Fluct. Drift Tot-Drift > > --- > Temperature 310 2.46886 2.46886 6.12135e-07 0.0171398 > T-Protein 310 32.1134 32.1117 -4.10352e-05 -1.14898 > T-Non-Protein 310 2.47549 2.47548 8.55869e-07 0.0239643 > -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20090917/08293573/attachment-0001.html -- Message: 4 Date: Thu, 17 Sep 2009 01:39:15 -0700 From: Darrell Koskinen Subject: [gmx-users] Periodic Boundary Conditions & Location of Atoms NearBox Edges To: gmx-users@gromacs.org Message-ID: <4ab1f5b3.5060...@ece.ubc.ca> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Dear GROMACS Gurus, In order to correctly model an infinite graphene sheet using periodic boundary conditions, should the box edges be located at the midpoints between the atomic bonds? Thanks. Darrell -- ___ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! End of gmx-users Digest, Vol 65, Issue 97 * ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Large fluctuation of protein temperature with nose hoover thermostat
The group PROTEIN isn't very large as the group NONPROTEIN, therefore its total kinetic energy fluctuates more. --Omer. On Wed, Sep 16, 2009 at 12:10, Stephane Abel wrote: > tc-grps = Protein Non-Protein ; two coupling groups - more accurate > tau_t = 0.4 0.4 ; time constant, in ps > ref_t = 310 310 ; reference temperature, one for each group, in K Energy Average RMSD Fluct. Drift Tot-Drift > > --- > Temperature 310 2.46886 2.46886 6.12135e-07 0.0171398 > T-Protein 310 32.1134 32.1117 -4.10352e-05 -1.14898 > T-Non-Protein 310 2.47549 2.47548 8.55869e-07 0.0239643 > ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Large fluctuation of protein temperature with nose hoover thermostat
Hi gromacs experts, For my simulations of peptide (8 AA) in water (5100, SPC/E) and with 1 Cl- i use the Nose-Hoover Thermostat to simulate in NVT ensemble. Since i am a beginner with GROMACS, i have a question with the tau_t parameters Parameters i used I ; Temperature coupling is on tcoupl = nose-hoover ; nose-hoover thermostat tc-grps = Protein Non-Protein ; two coupling groups - more accurate tau_t = 0.4 0.4 ; time constant, in ps ref_t = 310 310 ; reference temperature, one for each group, in K When i compute temperature (15, 40 and 41) of the system with g_energy for 30 ns, i obtain the following values. Energy Average RMSD Fluct. Drift Tot-Drift --- Temperature 310 2.46886 2.46886 6.12135e-07 0.0171398 T-Protein 310 32.1134 32.1117 -4.10352e-05 -1.14898 T-Non-Protein 310 2.47549 2.47548 8.55869e-07 0.0239643 Heat Capacity Cv: 12.473 J/mol K (factor = 6.34265e-05) gcq#109: "Ease Myself Into the Body Bag" (P.J. Harvey) As you can see the temp fluctuation is larger ( > 10 %) than the values for system and the solvent It is normal for you ? > If not how to correct it Thank in advance for your help ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
