[gmx-users] How to implement v-rescale thermostat in gromacs-3.3.3
Hi gmx-users, When I came across the 4.0 beta version, I found there was a new thermostat named v-rescale available here. I wonder if it would be easy to incorporate it in the version 3.3.3 as a patch. Note that the 4.0 version is still under development, I prefer to use a revised 3.3.3 version to make a production run. Thanks very much for your help. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Warning message with 3.3.3 but not with 3.3.1
Hi gmx-users, I want to simulate a solid/water interface. I just freeze the solid surface, and let the water molecules free to move. Here is a part of my mdp as follows: comm-mode = linear nstcomm = 10 comm-grps = SOL tcoupl = Berendsen tc-grps = SOL Solid tau-t = 0.1 0.1 ref-t = 298 0 Same system and same sets were tested both in gmx 3.3.1 and gmx 3.3.3. Following message in the log file was printed in the log file with gmx 3.3.3, but not with gmx 3.3.1. Large VCM(group rest): 0.1, -0.2, -0.0, T-cm: inf Large VCM(group rest): 0.1, -0.3, -0.0, T-cm: inf Large VCM(group rest): -0.0, -0.3, -0.0, T-cm: inf I wonder whether it is reasonable to stopcm or not. Would it cause any non-physical artifacts? Thanks for suggestions. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: infinite molecule problem - Follow up info
When I stopCM of the whole system, all running is ok, but I found the infinite surface oscillating along the xy plane collectively and frequently, so there were too much inconsistent shifts. Then I stopCM of the surface only, I get a lot of warnings about the Large VCM(group rest) (group rest = SOL in my system). Thanks for your attention. Stop COM of the whole system? 2008/4/6 Bo Zhou [EMAIL PROTECTED]: Dear gmx users, My previous question are: I want to simulate the solid/liquid interface, so I build an infinite inorganic molecule with pbc=full first. After I ran the system with vaccum (at the top of system) for a few ps, I found the crystal oscillating along the xy plane collectively and frequently, so there were too much inconsistent shifts. I wonder if it is reasonable, if not, is there any solution for it? Any suggestions would be helpful. Thanks. I have tested one system with infinite crystal only, and it turns out be to quite stable (no collective motion has been found), but when I put some water molecules on it, the crystal surface turns out to be what I have said above. Then I stop the COM motion of the crystal, and it seems ok again, just like what I have found in the simulation system with that crystal only (with stopcm too). However, I get a lot of warnings in the log file as follows: Large VCM(group rest): 0.00015, 0.00094, -0.00022, T-cm: inf Large VCM(group rest): -0.00038, 0.00063, -0.00140, T-cm: inf Large VCM(group rest): -0.00029, 0.00050, -0.00206, T-cm: inf Large VCM(group rest): 0.7, 0.00034, -0.00231, T-cm: inf Large VCM(group rest): 0.7, -0.00043, -0.00213, T-cm: inf .. I have not stop the COM motion of the group SOL, and I really do not know how to understand these warnings. I check the system again, everything seems alright except for these awkward warnings. I'm really out of ideas here. If anyone could give me some suggestions I would really appreciate it! Thanks for your time. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] infinite molecule problem
Dear gmx users, I want to simulate the solid/liquid interface, so I build an infinite inorganic molecule with pbc=full first. After I ran the system with vaccum (at the top of system) for a few ps, I found the crystal oscillating along the xy plane collectively and frequently, so there were too much inconsistent shifts. I wonder if it is reasonable, if not, is there any solution for it? Any suggestions would be helpful. Thanks. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] infinite molecule problem - Follow up info
Dear gmx users, My previous question are: I want to simulate the solid/liquid interface, so I build an infinite inorganic molecule with pbc=full first. After I ran the system with vaccum (at the top of system) for a few ps, I found the crystal oscillating along the xy plane collectively and frequently, so there were too much inconsistent shifts. I wonder if it is reasonable, if not, is there any solution for it? Any suggestions would be helpful. Thanks. I have tested one system with infinite crystal only, and it turns out be to quite stable (no collective motion has been found), but when I put some water molecules on it, the crystal surface turns out to be what I have said above. Then I stop the COM motion of the crystal, and it seems ok again, just like what I have found in the simulation system with that crystal only (with stopcm too). However, I get a lot of warnings in the log file as follows: Large VCM(group rest): 0.00015, 0.00094, -0.00022, T-cm: inf Large VCM(group rest): -0.00038, 0.00063, -0.00140, T-cm: inf Large VCM(group rest): -0.00029, 0.00050, -0.00206, T-cm: inf Large VCM(group rest): 0.7, 0.00034, -0.00231, T-cm: inf Large VCM(group rest): 0.7, -0.00043, -0.00213, T-cm: inf .. I have not stop the COM motion of the group SOL, and I really do not know how to understand these warnings. I check the system again, everything seems alright except for these awkward warnings. I'm really out of ideas here. If anyone could give me some suggestions I would really appreciate it! Thanks for your time. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] POL3 polarizable water model
Dear Gromacs users, I wonder whether or not the POL3 polarizable water model (Caldwell JW, Kollman PA (1995) J Phys Chem 99: 6208-6219.) can be incorporated in gmx with amber03 force field. Thanks in advance. Best regards ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Can 1-4 interactions be excluded seperately?
Hi all, There are two molecules in my system. One is parameterized with no torsion term in the energy expression (consistent with the OPLS force field), so 1-4 interactions should be excluded. The other one is treated as a normal protein molecule using OPLS force field. I want to include OPLS ff, but not to gen pairs with the previous molecule. Does it feasible in gmx? Thanks in advance. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Question about embedding a force field with no torsion term
Hi all, Recently I want to embed a force field ( Chem. Mater., 17 (23), 5658 -5669, 2005) in gmx. In the paper, It is said that the force field parameters are consistent with GROMACS. The energy expression has a form as follows: E= E(bond) + E(angle) + E(coulomb) + E(vdW) Note that there is no torsion term, I write an itp file manually and use nrexcel 2 in my molecule. I am not sure about how to deal with the 1-4 interactions, because when I include with the opls force field, gmx still generates 1-4 interactions. Is it necessary for having 1-4 interactions here? If necessary, how to make that force field consistent with opls ff ? Thanks in advance! ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Question about embedding a force field with no torsion term
Thanks, Mark. Can you tell me any more in detail? I am really somewhat confused about it. I want to cooperate this force field with oplsaa, but it looks strange that there is not any torsion energy at all but can have 1-4 interactions. with nrexcel=2, Do I still need 1-4 interactions made by the procedure of genning pairs? Thanks very much. Bo Zhou wrote: Hi all, Recently I want to embed a force field (/ Chem. Mater.,/ *17* (23), 5658 -5669, 2005) in gmx. In the paper, It is said that the force field parameters are consistent with GROMACS. The energy expression has a form as follows: E= E(bond) + E(angle) + E(coulomb) + E(vdW) Note that there is no torsion term, I write an itp file manually and use nrexcel 2 in my molecule. I am not sure about how to deal with the 1-4 interactions, because when I include with the opls force field, gmx still generates 1-4 interactions. Is it necessary for having 1-4 interactions here? If necessary, how to make that force field consistent with opls ff ? You can make it do what you want. See chapters 4 5 of the manual. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] surface tension calculation in g_energy
Hi all, I use the option #Surf*SurfTens in g_engery to calculate the surface tension, but I find that I really do not know how it works after I get some inconsistent results compared with the calculation using the formula gamma = 0.5*(Pzz - (Pxx+Pyy)/2) * Lz ( there are two surfaces here and the surfaces in normal to the Z-axis). Energy Average RMSD Fluct. Drift Tot-Drift --- #Surf*SurfTen1136.52557.05 2557 0.00852598 51.1559 == ### == A V E R A G E S == ### == Pressure (bar) -1.93061e+02 -6.88599e-01 -1.66823e-02 -6.84564e-01 -1.93953e+02 -2.93803e-02 7.79006e-03 -6.97915e-03 -9.87987e+01 The #Surf*SurfTens gives a value 568.25 bar*nm, and gamma = 0.5*(Pzz - (Pxx+Pyy)/2) * Lz gives a value 473.54 bar*nm. Please give me some suggestions about the inconsistency. Thanks in advance. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
