[gmx-users] Problem with output structures generated by energy minimization with GROMACS 4
Hi, I got a problem with the output structure files (gro/trr/xtc) generated by the energy minimization with GROMACS 4. That is, when I used the generated structure as the input for further minimizations or MD simulations, I got very large potential energy and forces at step 0, as if the structure had not been optimized at all. On the other hand, there is no problem when the input structure is taken from a previous MD run, and I got the expected potential at step 0. There is no problem, too, if I use GROMACS 3 to do the minimization. Any help is greatly appreciated! Hao Jiang -- 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] Problem with output structures generated by energy minimization with GROMACS 4
Tsjerk, Thanks for your reply. I am doing a simple test case with 500 SPC/E water molecules. First I did minimization with steepest decent, using a command like mdrun -pd -s water.gro.tpr -c final.gro The generated md.log looks like the following: Step Time Lambda 00.00.0 Energies (kJ/mol) LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential 4.70442e+03 -7.34875e+02 -2.65916e+04 -1.28439e+03 -2.39065e+04 Pressure (bar) 2.27899e+04 . . . Step Time Lambda 1000 1000.00.0 Energies (kJ/mol) LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential 5.53526e+03 -7.34875e+02 -3.22651e+04 -1.33018e+03 -2.87949e+04 Pressure (bar) 2.42765e+04 Steepest Descents did not converge to Fmax < 1 in 1001 steps. Potential Energy = -2.87949018657418e+04 Maximum force = 6.95206177080918e+01 on atom 1033 Norm of force = 3.71165837023948e+00 Just for testing I tried to do further optimization. I created a new tpr with the generated final.gro file and the old top and mdp files, then run mdrun again. This time the generated md.log looks like the following: === Step Time Lambda 00.00.0 Energies (kJ/mol) LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential 4.70442e+03 -7.34875e+02 -2.65916e+04 -1.28439e+03 -2.39065e+04 Pressure (bar) 2.27899e+04 . . . So it seems like final.gro has a potential energy that is very close to that of the original, un-optimized structure. While I repeat the same procedure with Gromacs 3.3, everything works as expected. For the first optimization I got --- Step Time Lambda 00.00.0 Energies (kJ/mol) LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential 4.70486e+03 -7.34875e+02 -2.65916e+04 -1.28441e+03 -2.39060e+04 Kinetic En. Total EnergyTemperature Pressure (bar) 0.0e+000.0e+000.0e+00 -1.63608e+03 . . . Step Time Lambda 999 999.00.0 Energies (kJ/mol) LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential 5.48610e+03 -7.34875e+02 -3.21894e+04 -1.29343e+03 -2.87316e+04 Kinetic En. Total EnergyTemperature Pressure (bar) 0.0e+000.0e+000.0e+00 -1.63608e+06 Step Time Lambda 1000 1000.00.0 Steepest Descents did not converge to Fmax < 1 in 1001 steps. Potential Energy = -2.87316123776041e+04 Maximum force = 2.72102300902620e+01 on atom 136 Norm of force = 2.08471187918543e+02 --- and for the further optimization I got === Step Time Lambda 00.00.0 Energies (kJ/mol) LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential 5.48626e+03 -7.34875e+02 -3.21871e+04 -1.29320e+03 -2.87289e+04 Kinetic En. Total EnergyTemperature Pressure (bar) 0.0e+000.0e+000.0e+00 -1.63608e+03 . . . === I don't know what causes the difference. Hao Jiang - Original Message - From: "Tsjerk Wassenaar" To: "Discussion list for GROMACS users" Sent: 2009年11月30日 12:37 PM Subject: Re: [gmx-users] Problem with output structures generated by energy minimization with GROMACS 4 Ni Hao, You don't give too much information here. What exactly are you doing? What are the commands? What's the difference between the first and the second pass of EM? One thing to check is whether the output/input file has a correct box definition. Cheers, Tsjerk 2009/11/30 HAO JIANG : > Hi, > > I got a problem with the output structure files (gro/trr/xtc) generated by > the energy minimization with GROMACS 4. That is, when I used the generated > structure as the input for further minimizations or MD simulations, I got > very large potential energy and forces at step 0, as if the structure had > not been optimized at all. On the other hand, there is no problem when > the input structure is taken from a previous MD run, and I got the expected > potential at step 0. There is no problem, too, if I use GROMACS 3 to do the > minimization. > > Any help is greatly appreciated! > > Hao Jiang > > -- > 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! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@grom
[gmx-users] Write the total dipole moment on-the-fly?
Dear All, Is there a way to let GROMACS to calculate and write the total dipole moment on-the-fly? I realize that g_dipoles can be used to calculate the total dipole moment using a stored trajectory. However, for a large system it is not very feasible to write the trajectory at a frequency good enough for spectra analysis. Thanks. Hao Jiang -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at 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
Re: [gmx-users] Re: gmx-users Dipole
Is the total dipole moment stored in the energy file of Gromacs 3.3 correct? Thanks. Hao -Original Message- From: David van der Spoel Sent: Sunday, November 27, 2011 9:36 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Re: gmx-users Dipole On 11/27/11 3:26 PM, Dr. Vitaly V. Chaban wrote: Dear All, Is there a way to let GROMACS to calculate and write the total dipole moment on-the-fly? I realize that g_dipoles can be used to calculate the total dipole moment using a stored trajectory. However, for a large system it is not very feasible to write the trajectory at a frequency good enough for spectra analysis. Thanks. I don't think such way exists, unless you insert the dipole calculation subroutine into the main code. All gromacs analysis tools imply postprocessing of the generated trajectories. In certain cases (e.g. when velocities or forces should be analyzed), this is not perfect, of course. This is stored in the energy file still, but THE NUMBERS ARE INCORRECT since gromacs 4.0. See http://redmine.gromacs.org/issues/620 -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at 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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at 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
[gmx-users] Umbrella sampling and WHAM along a curved pathway?
Dear all, I would like to calculate the PMF along a curved reaction pathway using umbrella sampling. I just wonder if it is appropriate to use g_wham to extract the PMF along the curved pathway? Any help would be appreciated. Hao Jiang -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at 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
[gmx-users] about the umbrella sampling potential
Dear all, I got confused about the usage of pull-geometry and pull-dim (pull-vector) settings in the umbrella sampling simulations (not the pull / SMD simulations). In an umbrella sampling potential, U(r)=0.5*(r-r0)*(r-r0), are r and r0 referring to (A) the distance between the pulled group and the reference group, or (B) the distance between the pulled group and the reference group *projected* to a vector pre-defined by pull-dim or pull-vector? Note these two distances are not equal unless the pulled group stay strictly on the predefined vector, which I believe is not always the case. If A is true, in principle group1 should be able to move freely within a spherical shell centered at group0, right? What is the point to specify pull-geometry and pull-dim in this case? If B is true, group1 should in principle be able to move freely in plane perpendicular to the pre-defined vector. So if pull-dim= N N Y, the pulled group should be able to move freely in the X-Y plane, right? Any help would be greatly appreciated! Hao Jiang -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at 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
Re: [gmx-users] Umbrella sampling and WHAM along a curved pathway?
Hi, Jochen, Thanks a lot for your reply. I looked at the example header provided by g_wham -h. I just wonder if you can answer some more questions for me. The example header is # UMBRELLA 3.0 # Component selection: 0 0 1 # nSkip 1 # Ref. Group 'TestAtom' # Nr. of pull groups 2 # Group 1 'GR1' Umb. Pos. 5.0 Umb. Cons. 1000.0 # Group 2 'GR2' Umb. Pos. 2.0 Umb. Cons. 500.0 # I guess following "# Component selection" one need to specify the Cartesian coordinate components in which the distance restraints are applied. In this example, I guess the restraint is applied in the Z coordinate, right? If, say, I want to put restraints in all three coordinates, X,Y, and Z, I need to put "1 1 1" here, right? In this case, there shall be 3 coordinates to specify the Umb. Pos., so I would put something like "# Group 1 'GR1' Umb. Pos. 5.0 5.0 5.0 Umb. Cons. 1000.0", assuming the force constant is same for X, Y, and Z. Am I right, or is there some other way to specify the position of the umbrella? And I should have 1 time column and 3 data columns/per-group following the headers, right? If, instead of using the pull code, I create by hands a set of initial configurations where the pull-groups are placed along a curved pathway, and use "pull_start = yes" with "pull_rate1 = 0", will GROMACS and g_wham automatically recognize the positions of the umbrellas from the initial configurations? Thank you very much! Hao On Thu, Feb 16, 2012 at 10:42 AM, Jochen Hub wrote: > Hi, > > since there is no pull type for curved pathways, you have to generate the > gmx3-type pdo files from your simlation output and use these in g_wham > (g_wham -ip). See g_wham -h for a example header of a pdo file. > > Cheers, > Jochen > > > > Am 2/14/12 5:53 PM, schrieb HAO JIANG: > >> Dear all, >> >> I would like to calculate the PMF along a curved reaction pathway >> using umbrella sampling. I just wonder if it is appropriate to use >> g_wham to extract the PMF along the curved pathway? Any help would be >> appreciated. >> >> Hao Jiang > > > -- > --- > Dr. Jochen Hub > Computational Molecular Biophysics Group > Institute for Microbiology and Genetics > Georg-August-University of Göttingen > Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. > Phone: +49-551-39-14189 > http://cmb.bio.uni-goettingen.de/ > --- > -- > 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/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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at 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
