Re: [gmx-users] questions about energy minimization
On 14/04/2010 1:28 PM, DreamCatcher wrote: To whom may be concerned, I am just doing an energy minimization on a polymer chain ---PVA, which contains 50 repeat units. I am puzzled about how to choose an appropriate emtol. It's said to be a maximum force in the system. But how to make sure that the emtol I choose is big or small enough that my system will finally well equilibrium? That depends on the purpose to which you intend to put it. For preparation for MD, so long as the subsequent equilibration process doesn't explode, you minimized enough. After I finished the energy minimization, when the maximum force is actually under the emmtol, I compare the potential to a previou energy minimization work using some other software like Material Studio, It is the finally potential that surprise me a lot. The potential I get using gromacs is still positive and with a magnitude of e~03 whist using Material Studio it is negative and with the same magnitude.Why so? Is there any reference I can refer to? That will mean you have something nonphysical in your structure file (e.g. overlapping atoms) or model physics (broken parameters or file formats). In such cases EM may or may not help. Mark -- 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] OpenMM
Hi, thanks a lot for your answer, but I have some doubts yet... My .gro files are very different and I'm not sure that the architecture (CPU / GPU) could influence the result so much as in my example (the first is the output of the serial code and the second that of the parallel ones). SERIAL CODE: 1LYSH N1 3.240 2.123 0.830 0.0828 0.7601 -0.2788 1LYSHCA2 3.114 2.170 0.777 -0.1210 0.1179 -0.3660 1LYSHCB3 3.060 2.258 0.889 -0.1060 0.0142 -0.2772 1LYSHCG4 3.103 2.403 0.867 -1.1970 0.3922 0.0170 1LYSHCD5 3.078 2.498 0.983 -0.5172 1.0015 -0.3267 1LYSHCE6 3.120 2.451 1.122 -0.5706 0.5624 -0.4567 1LYSHNZ7 3.024 2.505 1.220 0.2425 1.4466 -0.1367 1LYSH C8 3.006 2.065 0.754 0.1697 -0.4396 0.7191 1LYSH O9 2.896 2.086 0.701 0.0216 -1.3952 0.6269 2VAL N 10 3.036 1.943 0.799 0.5429 -0.4260 0.5099 2VAL H 11 3.132 1.933 0.831 0.8289 0.8067 0.0933 2VAL CA 12 2.955 1.826 0.822 0.2219 -0.3946 -0.4277 PARALLEL CODE: 1LYSH N1 3.333 1.969 0.702 -0.4164 -0.1749 -0.1669 1LYSHCA2 3.221 2.054 0.737 -0.0727 0.2241 -0.0385 1LYSHCB3 3.163 2.122 0.613 -0.1387 -0.2965 -0.2935 1LYSHCG4 3.219 2.261 0.586 0.0989 -0.2444 0.4520 1LYSHCD5 3.100 2.352 0.558 0.5215 0.0874 -0.3041 1LYSHCE6 3.123 2.486 0.627 -0.1705 0.3629 -0.6025 1LYSHNZ7 2.996 2.514 0.696 -0.2146 0.6887 -0.8084 1LYSH C8 3.110 1.973 0.800 -0.1975 -0.0906 -0.6520 1LYSH O9 3.007 2.030 0.837 0.2640 0.4243 -0.1313 2VAL N 10 3.141 1.849 0.840 0.2749 -0.0187 -0.7992 2VAL H 11 3.238 1.824 0.826 0.5334 0.1303 0.6497 2VAL CA 12 3.050 1.754 0.901 0.8255 0.0012 0.0684 Then, even if in the .log file (parallel code), the energy terms are null at every time step to avoid slow communication between GPU and CPU, the average energies are null too. (I have test this also using g_energy) AVERAGES: Energies (kJ/mol) AngleProper Dih. Ryckaert-Bell. LJ-14 Coulomb-14 0.0e+000.0e+000.0e+00 0.0e+000.0e+00 LJ (SR) Coulomb (SR) RF excl. PotentialKinetic En. 0.0e+000.0e+000.0e+00 -1.05419e+065.24361e+05 Total EnergyTemperature Pressure (bar) Cons. rmsd () -5.29827e+053.39337e+040.0e+00 0.0e+00 Thanks in advance, Giulia On Tue, 13 Apr 2010 19:14:29 +0200 Rossen Apostolov rossen.aposto...@cbr.su.se wrote: Hi,O On 04/13/2010 04:23 PM, PACIELLO GIULIA wrote: Even if I have followed all the instructions reported for the correct installation of GPU, CUDA, OpenMM and even if my .mdp file for the simulation is written following the features supported in the release Gromacs-OpenMM, the output of the serial code running on CPU is quite different from that of the parallel code running on GPU (.gro files). That is normal. The architectures are different and the algorithms are different so you can't expect numerically identical results. The simulated ensembles should be properly generated though. Looking at the .log file I have also noticed that the energy terms 'Angle', 'Proper Dih.''Ryckaert-Bell.','LJ-14'Coulomb-14', 'LJ (SR)', 'Coulomb (SR), 'RF excl', are null for the simulation performed with the parallel code. OpenMM doesn't report individual energy and force terms, only the totals. This is done for efficiency reasons - it saves GPU memory and avoids slow CPU-GPU transfers. Rossen -- 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 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] OpenMM
On 14/04/2010 4:31 PM, PACIELLO GIULIA wrote: Hi, thanks a lot for your answer, but I have some doubts yet... My .gro files are very different and I'm not sure that the architecture (CPU / GPU) could influence the result so much as in my example (the first is the output of the serial code and the second that of the parallel ones). MD is chaotic. Tiny differences at an early stage lead to wildly different results later. That's inevitable. However ensemble averages should converge to the same value. SERIAL CODE: 1LYSH N 1 3.240 2.123 0.830 0.0828 0.7601 -0.2788 1LYSH CA 2 3.114 2.170 0.777 -0.1210 0.1179 -0.3660 1LYSH CB 3 3.060 2.258 0.889 -0.1060 0.0142 -0.2772 1LYSH CG 4 3.103 2.403 0.867 -1.1970 0.3922 0.0170 1LYSH CD 5 3.078 2.498 0.983 -0.5172 1.0015 -0.3267 1LYSH CE 6 3.120 2.451 1.122 -0.5706 0.5624 -0.4567 1LYSH NZ 7 3.024 2.505 1.220 0.2425 1.4466 -0.1367 1LYSH C 8 3.006 2.065 0.754 0.1697 -0.4396 0.7191 1LYSH O 9 2.896 2.086 0.701 0.0216 -1.3952 0.6269 2VAL N 10 3.036 1.943 0.799 0.5429 -0.4260 0.5099 2VAL H 11 3.132 1.933 0.831 0.8289 0.8067 0.0933 2VAL CA 12 2.955 1.826 0.822 0.2219 -0.3946 -0.4277 PARALLEL CODE: 1LYSH N 1 3.333 1.969 0.702 -0.4164 -0.1749 -0.1669 1LYSH CA 2 3.221 2.054 0.737 -0.0727 0.2241 -0.0385 1LYSH CB 3 3.163 2.122 0.613 -0.1387 -0.2965 -0.2935 1LYSH CG 4 3.219 2.261 0.586 0.0989 -0.2444 0.4520 1LYSH CD 5 3.100 2.352 0.558 0.5215 0.0874 -0.3041 1LYSH CE 6 3.123 2.486 0.627 -0.1705 0.3629 -0.6025 1LYSH NZ 7 2.996 2.514 0.696 -0.2146 0.6887 -0.8084 1LYSH C 8 3.110 1.973 0.800 -0.1975 -0.0906 -0.6520 1LYSH O 9 3.007 2.030 0.837 0.2640 0.4243 -0.1313 2VAL N 10 3.141 1.849 0.840 0.2749 -0.0187 -0.7992 2VAL H 11 3.238 1.824 0.826 0.5334 0.1303 0.6497 2VAL CA 12 3.050 1.754 0.901 0.8255 0.0012 0.0684 Then, even if in the .log file (parallel code), the energy terms are null at every time step to avoid slow communication between GPU and CPU, the average energies are null too. (I have test this also using g_energy) AVERAGES: Energies (kJ/mol) Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14 0.0e+00 0.0e+00 0.0e+00 0.0e+00 0.0e+00 LJ (SR) Coulomb (SR) RF excl. Potential Kinetic En. 0.0e+00 0.0e+00 0.0e+00 -1.05419e+06 5.24361e+05 Total Energy Temperature Pressure (bar) Cons. rmsd () -5.29827e+05 3.39337e+04 0.0e+00 0.0e+00 There's no evidence of a problem here, given that because the GPU version will not report such energies, there's nothing to average. Mark -- 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] OpenMM
Ok...so how could I know the energies among atoms? And how can I test if my parallel code is running in the correct manner? Thanks, Giulia On Wed, 14 Apr 2010 16:43:13 +1000 Mark Abraham mark.abra...@anu.edu.au wrote: On 14/04/2010 4:31 PM, PACIELLO GIULIA wrote: Hi, thanks a lot for your answer, but I have some doubts yet... My .gro files are very different and I'm not sure that the architecture (CPU / GPU) could influence the result so much as in my example (the first is the output of the serial code and the second that of the parallel ones). MD is chaotic. Tiny differences at an early stage lead to wildly different results later. That's inevitable. However ensemble averages should converge to the same value. SERIAL CODE: 1LYSH N 1 3.240 2.123 0.830 0.0828 0.7601 -0.2788 1LYSH CA 2 3.114 2.170 0.777 -0.1210 0.1179 -0.3660 1LYSH CB 3 3.060 2.258 0.889 -0.1060 0.0142 -0.2772 1LYSH CG 4 3.103 2.403 0.867 -1.1970 0.3922 0.0170 1LYSH CD 5 3.078 2.498 0.983 -0.5172 1.0015 -0.3267 1LYSH CE 6 3.120 2.451 1.122 -0.5706 0.5624 -0.4567 1LYSH NZ 7 3.024 2.505 1.220 0.2425 1.4466 -0.1367 1LYSH C 8 3.006 2.065 0.754 0.1697 -0.4396 0.7191 1LYSH O 9 2.896 2.086 0.701 0.0216 -1.3952 0.6269 2VAL N 10 3.036 1.943 0.799 0.5429 -0.4260 0.5099 2VAL H 11 3.132 1.933 0.831 0.8289 0.8067 0.0933 2VAL CA 12 2.955 1.826 0.822 0.2219 -0.3946 -0.4277 PARALLEL CODE: 1LYSH N 1 3.333 1.969 0.702 -0.4164 -0.1749 -0.1669 1LYSH CA 2 3.221 2.054 0.737 -0.0727 0.2241 -0.0385 1LYSH CB 3 3.163 2.122 0.613 -0.1387 -0.2965 -0.2935 1LYSH CG 4 3.219 2.261 0.586 0.0989 -0.2444 0.4520 1LYSH CD 5 3.100 2.352 0.558 0.5215 0.0874 -0.3041 1LYSH CE 6 3.123 2.486 0.627 -0.1705 0.3629 -0.6025 1LYSH NZ 7 2.996 2.514 0.696 -0.2146 0.6887 -0.8084 1LYSH C 8 3.110 1.973 0.800 -0.1975 -0.0906 -0.6520 1LYSH O 9 3.007 2.030 0.837 0.2640 0.4243 -0.1313 2VAL N 10 3.141 1.849 0.840 0.2749 -0.0187 -0.7992 2VAL H 11 3.238 1.824 0.826 0.5334 0.1303 0.6497 2VAL CA 12 3.050 1.754 0.901 0.8255 0.0012 0.0684 Then, even if in the .log file (parallel code), the energy terms are null at every time step to avoid slow communication between GPU and CPU, the average energies are null too. (I have test this also using g_energy) AVERAGES: Energies (kJ/mol) Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14 0.0e+00 0.0e+00 0.0e+00 0.0e+00 0.0e+00 LJ (SR) Coulomb (SR) RF excl. Potential Kinetic En. 0.0e+00 0.0e+00 0.0e+00 -1.05419e+06 5.24361e+05 Total Energy Temperature Pressure (bar) Cons. rmsd () -5.29827e+05 3.39337e+04 0.0e+00 0.0e+00 There's no evidence of a problem here, given that because the GPU version will not report such energies, there's nothing to average. Mark -- 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 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] OpenMM
On 14/04/2010 4:52 PM, PACIELLO GIULIA wrote: Ok...so how could I know the energies among atoms? Since it's not reported, you can't get breakdowns of energies. That's a limitation from the use of GPU. If you want this information, perhaps do your simulation on the GPU and re-rerun selected frames from your trajectory on a different machine that does not use GPUs. And how can I test if my parallel code is running in the correct manner? MD is chaotic. Tiny differences at an early stage lead to wildly different results later. That's inevitable. However ensemble averages should converge to the same value. Do things converge to the same values? There's a chance that mdrun -reprod will lead to equivalent total energies after only one step, if that's been implemented that way. Mark -- 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] OpenMM
I dont'know if this is the right way to test that things converge to the same value...but I have made an energy minimization on CPU of the two output (parallel and serial). I have obtained this results: FROM PARALLEL OUTPUT Potential Energy = -1.6960029e+04 Maximum force = 1.7282695e+03 on atom 364 Norm of force = 4.6171844e+02 FROM SERIAL OUTPUT Potential Energy = -1.7814945e+04 Maximum force = 2.1551072e+03 on atom 496 Norm of force = 2.9537823e+02 Thanks, Giulia On Wed, 14 Apr 2010 16:58:37 +1000 Mark Abraham mark.abra...@anu.edu.au wrote: On 14/04/2010 4:52 PM, PACIELLO GIULIA wrote: Ok...so how could I know the energies among atoms? Since it's not reported, you can't get breakdowns of energies. That's a limitation from the use of GPU. If you want this information, perhaps do your simulation on the GPU and re-rerun selected frames from your trajectory on a different machine that does not use GPUs. And how can I test if my parallel code is running in the correct manner? MD is chaotic. Tiny differences at an early stage lead to wildly different results later. That's inevitable. However ensemble averages should converge to the same value. Do things converge to the same values? There's a chance that mdrun -reprod will lead to equivalent total energies after only one step, if that's been implemented that way. Mark -- 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 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] Re: small help
Again, it is better to post these question on the gromacs list. You'll find more people able to help you and the exchange might be profitable to others. I am not sure what you want to do! Please explain what you want to do and what has failed to give you the answer you are looking for. XAvier. On Apr 14, 2010, at 7:23 AM, satish kumar ainala wrote: Dear sir , I was not able to find the correct parameters for running this command g_rmsdist for atompair distances . so please kindly send me the syntax for running this command for Atompair distances. I searched for mailing list but i cound not get . Yours Obediently satish kumar -- 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] OpenMM
On 14/04/2010 5:18 PM, PACIELLO GIULIA wrote: I dont'know if this is the right way to test that things converge to the same value...but I have made an energy minimization on CPU of the two output (parallel and serial). I have obtained this results: FROM PARALLEL OUTPUT Potential Energy = -1.6960029e+04 Maximum force = 1.7282695e+03 on atom 364 Norm of force = 4.6171844e+02 FROM SERIAL OUTPUT Potential Energy = -1.7814945e+04 Maximum force = 2.1551072e+03 on atom 496 Norm of force = 2.9537823e+02 They're probably both fine. By converged I was referring to an equilibrium MD ensemble. Mark -- 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] OpenMM
Well, I have used the option -rerun to 'rerun' on CPU the simulation from the parallel code. As you can see in the following tables, results are very similar for non bonded terms, but not for the other energetic terms (these are avereges obtained from g_energy): PARALLEL CODE Angle: 4256.27 Prop-di: 322.302 R-B: 3101.14 LJ-14: 2107.6 Coul-14: 15212 LJ(SR): -3410.22 Coul(SR): -29368.3 RF(excl): -9425.23 Pot.En: -17204.5 Kin.En:5243.87 Tot.En: -11960.6 SERIAL CODE: Angle: 6089.56 Prop-di: 466.121 R-B: 3677.95 LJ-14: 2234.85 Coul-14: 15149.8 LJ(SR): -3144 Coul(SR): -29240.7 RF(excl): -9425.25 Pot.En: -14191.7 Kin.En:8262.96 Tot.En: -5929.78 I can't use the -reprod option, but I have noticed that the .gro files after the energy minimization are very similar (I have performed this minimization on the .gro files obtained running the parallel and serial codes)...systems are converging to the same equilibrium ensamble? I'm thankful for your help, Giulia On Wed, 14 Apr 2010 18:03:43 +1000 Mark Abraham mark.abra...@anu.edu.au wrote: On 14/04/2010 5:18 PM, PACIELLO GIULIA wrote: I dont'know if this is the right way to test that things converge to the same value...but I have made an energy minimization on CPU of the two output (parallel and serial). I have obtained this results: FROM PARALLEL OUTPUT Potential Energy = -1.6960029e+04 Maximum force = 1.7282695e+03 on atom 364 Norm of force = 4.6171844e+02 FROM SERIAL OUTPUT Potential Energy = -1.7814945e+04 Maximum force = 2.1551072e+03 on atom 496 Norm of force = 2.9537823e+02 They're probably both fine. By converged I was referring to an equilibrium MD ensemble. Mark -- 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 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] Hydrogens missing during parameterization
Hi ALL, I have a ligand LDOPA with 25 atoms (including all hydrogens).: --- DAH COORDS 25 1DAH O1 5.988 5.216 9.128 1DAH C2 5.980 5.110 9.194 1DAH OXT 3 5.951 4.985 9.139 1DAH CA 4 6.001 5.107 9.349 1DAH HA 5 5.935 5.027 9.384 1DAH N6 6.140 5.064 9.387 1DAH H2 7 6.161 4.977 9.343 1DAH H3 8 6.137 5.056 9.486 1DAH H1 9 6.206 5.133 9.356 1DAH CB 10 5.952 5.236 9.422 1DAH HB1 11 5.985 5.320 9.362 1DAH HB2 12 5.999 5.231 9.520 1DAH CG 13 5.802 5.258 9.450 1DAH CD2 14 5.761 5.333 9.565 1DAH HD2 15 5.836 5.375 9.632 1DAH CE2 16 5.623 5.353 9.592 1DAH OE2 17 5.589 5.425 9.704 1DAH HE2 18 5.672 5.454 9.752 1DAH CZ 19 5.523 5.297 9.503 1DAH OZ 20 5.387 5.314 9.525 1DAH HZ 21 5.335 5.268 9.453 1DAH CE1 22 5.564 5.223 9.389 1DAH HE1 23 5.489 5.181 9.321 1DAH CD1 24 5.701 5.203 9.362 1DAH HD1 25 5.731 5.146 9.274 1.02033 1.02033 1.02033 I derived the topology file from PRODRG server. However the .itp file is giving only 22 atoms definition and 3 of the hydrogen atoms are missing: - DAH 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1OM 1 DAH O 1 -0.715 15.9994 2 C 1 DAH C 10.387 12.0110 3OM 1 DAH OXT 1 -0.716 15.9994 4 CH1 1 DAH CA 10.178 13.0190 5NL 1 DAH N 10.683 14.0067 6 H 1 DAH H2 10.010 1.0080 7 H 1 DAH H3 10.010 1.0080 8 H 1 DAH H1 10.011 1.0080 9 CH2 1 DAH CB 10.152 14.0270 10 C 1 DAH CG 2 -0.020 12.0110 11 CR1 1 DAH CD2 20.001 12.0110 12HC 1 DAH HD2 20.019 1.0080 13 C 1 DAH CE2 30.130 12.0110 14OA 1 DAH OE2 3 -0.197 15.9994 15 H 1 DAH HE2 30.051 1.0080 16 C 1 DAH CZ 30.130 12.0110 17OA 1 DAH OZ 3 -0.197 15.9994 18 H 1 DAH HZ 30.051 1.0080 19 CR1 1 DAH CE1 30.001 12.0110 20HC 1 DAH HE1 30.031 1.0080 21 CR1 1 DAH CD1 40.000 12.0110 22HC 1 DAH HD1 40.000 1.0080 [ bonds ] So you can see that HA, HB2 and HB3 hydrogens are missing here. So I am getting error messages popped by grompp commands. How can I get the definition of those missing 3 H atoms? Is it ok if I delete those 3 H atoms from my .gro file and proceed? If not then how to derive parameters for them? Any suggestion is welcome. Thanks a lot in advance. Regards, Anirban -- 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] Hydrogens missing during parameterization
You are missing HB1 and HB2, not HB2 and HB3 :)) This is due to the force field our are using. Gromos I presume: it uses the united H idea: non-polar H are not explicitly modeled. you should be able to erase those from your gro file, but I would suggest you get into some literature about the FF you use. XAvier. On Apr 14, 2010, at 11:36 AM, Anirban Ghosh wrote: Hi ALL, I have a ligand LDOPA with 25 atoms (including all hydrogens).: --- DAH COORDS 25 1DAH O1 5.988 5.216 9.128 1DAH C2 5.980 5.110 9.194 1DAH OXT 3 5.951 4.985 9.139 1DAH CA 4 6.001 5.107 9.349 1DAH HA 5 5.935 5.027 9.384 1DAH N6 6.140 5.064 9.387 1DAH H2 7 6.161 4.977 9.343 1DAH H3 8 6.137 5.056 9.486 1DAH H1 9 6.206 5.133 9.356 1DAH CB 10 5.952 5.236 9.422 1DAH HB1 11 5.985 5.320 9.362 1DAH HB2 12 5.999 5.231 9.520 1DAH CG 13 5.802 5.258 9.450 1DAH CD2 14 5.761 5.333 9.565 1DAH HD2 15 5.836 5.375 9.632 1DAH CE2 16 5.623 5.353 9.592 1DAH OE2 17 5.589 5.425 9.704 1DAH HE2 18 5.672 5.454 9.752 1DAH CZ 19 5.523 5.297 9.503 1DAH OZ 20 5.387 5.314 9.525 1DAH HZ 21 5.335 5.268 9.453 1DAH CE1 22 5.564 5.223 9.389 1DAH HE1 23 5.489 5.181 9.321 1DAH CD1 24 5.701 5.203 9.362 1DAH HD1 25 5.731 5.146 9.274 1.02033 1.02033 1.02033 I derived the topology file from PRODRG server. However the .itp file is giving only 22 atoms definition and 3 of the hydrogen atoms are missing: - DAH 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1OM 1 DAH O 1 -0.715 15.9994 2 C 1 DAH C 10.387 12.0110 3OM 1 DAH OXT 1 -0.716 15.9994 4 CH1 1 DAH CA 10.178 13.0190 5NL 1 DAH N 10.683 14.0067 6 H 1 DAH H2 10.010 1.0080 7 H 1 DAH H3 10.010 1.0080 8 H 1 DAH H1 10.011 1.0080 9 CH2 1 DAH CB 10.152 14.0270 10 C 1 DAH CG 2 -0.020 12.0110 11 CR1 1 DAH CD2 20.001 12.0110 12HC 1 DAH HD2 20.019 1.0080 13 C 1 DAH CE2 30.130 12.0110 14OA 1 DAH OE2 3 -0.197 15.9994 15 H 1 DAH HE2 30.051 1.0080 16 C 1 DAH CZ 30.130 12.0110 17OA 1 DAH OZ 3 -0.197 15.9994 18 H 1 DAH HZ 30.051 1.0080 19 CR1 1 DAH CE1 30.001 12.0110 20HC 1 DAH HE1 30.031 1.0080 21 CR1 1 DAH CD1 40.000 12.0110 22HC 1 DAH HD1 40.000 1.0080 [ bonds ] So you can see that HA, HB2 and HB3 hydrogens are missing here. So I am getting error messages popped by grompp commands. How can I get the definition of those missing 3 H atoms? Is it ok if I delete those 3 H atoms from my .gro file and proceed? If not then how to derive parameters for them? Any suggestion is welcome. Thanks a lot in advance. Regards, Anirban -- 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 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] Hydrogens missing during parameterization
Hi, XAvier, Sorry for that mistake. Yes, exactly PRODRG is not giving the non-polar hydrogens. There I am using the GROMOS96.1 FF. So is there any way to get the proper .itp file? I mean any other online server like PRODRG? Or How can I derive the proper .itp file manually? Any suggestion is welcome. Thanks a lot for the prompt reply. Regards, Anirban On Wed, Apr 14, 2010 at 3:25 PM, XAvier Periole x.peri...@rug.nl wrote: You are missing HB1 and HB2, not HB2 and HB3 :)) This is due to the force field our are using. Gromos I presume: it uses the united H idea: non-polar H are not explicitly modeled. you should be able to erase those from your gro file, but I would suggest you get into some literature about the FF you use. XAvier. On Apr 14, 2010, at 11:36 AM, Anirban Ghosh wrote: Hi ALL, I have a ligand LDOPA with 25 atoms (including all hydrogens).: --- DAH COORDS 25 1DAH O1 5.988 5.216 9.128 1DAH C2 5.980 5.110 9.194 1DAH OXT 3 5.951 4.985 9.139 1DAH CA 4 6.001 5.107 9.349 1DAH HA 5 5.935 5.027 9.384 1DAH N6 6.140 5.064 9.387 1DAH H2 7 6.161 4.977 9.343 1DAH H3 8 6.137 5.056 9.486 1DAH H1 9 6.206 5.133 9.356 1DAH CB 10 5.952 5.236 9.422 1DAH HB1 11 5.985 5.320 9.362 1DAH HB2 12 5.999 5.231 9.520 1DAH CG 13 5.802 5.258 9.450 1DAH CD2 14 5.761 5.333 9.565 1DAH HD2 15 5.836 5.375 9.632 1DAH CE2 16 5.623 5.353 9.592 1DAH OE2 17 5.589 5.425 9.704 1DAH HE2 18 5.672 5.454 9.752 1DAH CZ 19 5.523 5.297 9.503 1DAH OZ 20 5.387 5.314 9.525 1DAH HZ 21 5.335 5.268 9.453 1DAH CE1 22 5.564 5.223 9.389 1DAH HE1 23 5.489 5.181 9.321 1DAH CD1 24 5.701 5.203 9.362 1DAH HD1 25 5.731 5.146 9.274 1.02033 1.02033 1.02033 I derived the topology file from PRODRG server. However the .itp file is giving only 22 atoms definition and 3 of the hydrogen atoms are missing: - DAH 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1OM 1 DAH O 1 -0.715 15.9994 2 C 1 DAH C 10.387 12.0110 3OM 1 DAH OXT 1 -0.716 15.9994 4 CH1 1 DAH CA 10.178 13.0190 5NL 1 DAH N 10.683 14.0067 6 H 1 DAH H2 10.010 1.0080 7 H 1 DAH H3 10.010 1.0080 8 H 1 DAH H1 10.011 1.0080 9 CH2 1 DAH CB 10.152 14.0270 10 C 1 DAH CG 2 -0.020 12.0110 11 CR1 1 DAH CD2 20.001 12.0110 12HC 1 DAH HD2 20.019 1.0080 13 C 1 DAH CE2 30.130 12.0110 14OA 1 DAH OE2 3 -0.197 15.9994 15 H 1 DAH HE2 30.051 1.0080 16 C 1 DAH CZ 30.130 12.0110 17OA 1 DAH OZ 3 -0.197 15.9994 18 H 1 DAH HZ 30.051 1.0080 19 CR1 1 DAH CE1 30.001 12.0110 20HC 1 DAH HE1 30.031 1.0080 21 CR1 1 DAH CD1 40.000 12.0110 22HC 1 DAH HD1 40.000 1.0080 [ bonds ] So you can see that HA, HB2 and HB3 hydrogens are missing here. So I am getting error messages popped by grompp commands. How can I get the definition of those missing 3 H atoms? Is it ok if I delete those 3 H atoms from my .gro file and proceed? If not then how to derive parameters for them? Any suggestion is welcome. Thanks a lot in advance. Regards, Anirban -- 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
Re: [gmx-users] Hydrogens missing during parameterization
You have the proper itp file for the GROMOS FF. Some H are not explicitly described! On Apr 14, 2010, at 12:05 PM, Anirban Ghosh wrote: Hi, XAvier, Sorry for that mistake. Yes, exactly PRODRG is not giving the non- polar hydrogens. There I am using the GROMOS96.1 FF. So is there any way to get the proper .itp file? I mean any other online server like PRODRG? Or How can I derive the proper .itp file manually? Any suggestion is welcome. Thanks a lot for the prompt reply. Regards, Anirban On Wed, Apr 14, 2010 at 3:25 PM, XAvier Periole x.peri...@rug.nl wrote: You are missing HB1 and HB2, not HB2 and HB3 :)) This is due to the force field our are using. Gromos I presume: it uses the united H idea: non-polar H are not explicitly modeled. you should be able to erase those from your gro file, but I would suggest you get into some literature about the FF you use. XAvier. On Apr 14, 2010, at 11:36 AM, Anirban Ghosh wrote: Hi ALL, I have a ligand LDOPA with 25 atoms (including all hydrogens).: --- DAH COORDS 25 1DAH O1 5.988 5.216 9.128 1DAH C2 5.980 5.110 9.194 1DAH OXT 3 5.951 4.985 9.139 1DAH CA 4 6.001 5.107 9.349 1DAH HA 5 5.935 5.027 9.384 1DAH N6 6.140 5.064 9.387 1DAH H2 7 6.161 4.977 9.343 1DAH H3 8 6.137 5.056 9.486 1DAH H1 9 6.206 5.133 9.356 1DAH CB 10 5.952 5.236 9.422 1DAH HB1 11 5.985 5.320 9.362 1DAH HB2 12 5.999 5.231 9.520 1DAH CG 13 5.802 5.258 9.450 1DAH CD2 14 5.761 5.333 9.565 1DAH HD2 15 5.836 5.375 9.632 1DAH CE2 16 5.623 5.353 9.592 1DAH OE2 17 5.589 5.425 9.704 1DAH HE2 18 5.672 5.454 9.752 1DAH CZ 19 5.523 5.297 9.503 1DAH OZ 20 5.387 5.314 9.525 1DAH HZ 21 5.335 5.268 9.453 1DAH CE1 22 5.564 5.223 9.389 1DAH HE1 23 5.489 5.181 9.321 1DAH CD1 24 5.701 5.203 9.362 1DAH HD1 25 5.731 5.146 9.274 1.02033 1.02033 1.02033 I derived the topology file from PRODRG server. However the .itp file is giving only 22 atoms definition and 3 of the hydrogen atoms are missing: - DAH 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1OM 1 DAH O 1 -0.715 15.9994 2 C 1 DAH C 10.387 12.0110 3OM 1 DAH OXT 1 -0.716 15.9994 4 CH1 1 DAH CA 10.178 13.0190 5NL 1 DAH N 10.683 14.0067 6 H 1 DAH H2 10.010 1.0080 7 H 1 DAH H3 10.010 1.0080 8 H 1 DAH H1 10.011 1.0080 9 CH2 1 DAH CB 10.152 14.0270 10 C 1 DAH CG 2 -0.020 12.0110 11 CR1 1 DAH CD2 20.001 12.0110 12HC 1 DAH HD2 20.019 1.0080 13 C 1 DAH CE2 30.130 12.0110 14OA 1 DAH OE2 3 -0.197 15.9994 15 H 1 DAH HE2 30.051 1.0080 16 C 1 DAH CZ 30.130 12.0110 17OA 1 DAH OZ 3 -0.197 15.9994 18 H 1 DAH HZ 30.051 1.0080 19 CR1 1 DAH CE1 30.001 12.0110 20HC 1 DAH HE1 30.031 1.0080 21 CR1 1 DAH CD1 40.000 12.0110 22HC 1 DAH HD1 40.000 1.0080 [ bonds ] So you can see that HA, HB2 and HB3 hydrogens are missing here. So I am getting error messages popped by grompp commands. How can I get the definition of those missing 3 H atoms? Is it ok if I delete those 3 H atoms from my .gro file and proceed? If not then how to derive parameters for them? Any suggestion is welcome. Thanks a lot in advance. Regards, Anirban -- 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
Re: [gmx-users] Hydrogens missing during parameterization
Hi XAvier, Thanks for the reply. Actually I want to use this ligand with a protein and run the complex using ffG43a2 force-field of GROMACS4.0.7. So is it correct to leave away those 3 hydrogens HA, HB1 and HB2, which are not explicitly described? Because in protein-ligand complexes, hydrogen bond formations between the ligand and the protein are important? So should I continue with this .itp file with 3 less hydrogens? Thanks again. Regards, Anirban On Wed, Apr 14, 2010 at 3:50 PM, XAvier Periole x.peri...@rug.nl wrote: You have the proper itp file for the GROMOS FF. Some H are not explicitly described! On Apr 14, 2010, at 12:05 PM, Anirban Ghosh wrote: Hi, XAvier, Sorry for that mistake. Yes, exactly PRODRG is not giving the non-polar hydrogens. There I am using the GROMOS96.1 FF. So is there any way to get the proper .itp file? I mean any other online server like PRODRG? Or How can I derive the proper .itp file manually? Any suggestion is welcome. Thanks a lot for the prompt reply. Regards, Anirban On Wed, Apr 14, 2010 at 3:25 PM, XAvier Periole x.peri...@rug.nl wrote: You are missing HB1 and HB2, not HB2 and HB3 :)) This is due to the force field our are using. Gromos I presume: it uses the united H idea: non-polar H are not explicitly modeled. you should be able to erase those from your gro file, but I would suggest you get into some literature about the FF you use. XAvier. On Apr 14, 2010, at 11:36 AM, Anirban Ghosh wrote: Hi ALL, I have a ligand LDOPA with 25 atoms (including all hydrogens).: --- DAH COORDS 25 1DAH O1 5.988 5.216 9.128 1DAH C2 5.980 5.110 9.194 1DAH OXT 3 5.951 4.985 9.139 1DAH CA 4 6.001 5.107 9.349 1DAH HA 5 5.935 5.027 9.384 1DAH N6 6.140 5.064 9.387 1DAH H2 7 6.161 4.977 9.343 1DAH H3 8 6.137 5.056 9.486 1DAH H1 9 6.206 5.133 9.356 1DAH CB 10 5.952 5.236 9.422 1DAH HB1 11 5.985 5.320 9.362 1DAH HB2 12 5.999 5.231 9.520 1DAH CG 13 5.802 5.258 9.450 1DAH CD2 14 5.761 5.333 9.565 1DAH HD2 15 5.836 5.375 9.632 1DAH CE2 16 5.623 5.353 9.592 1DAH OE2 17 5.589 5.425 9.704 1DAH HE2 18 5.672 5.454 9.752 1DAH CZ 19 5.523 5.297 9.503 1DAH OZ 20 5.387 5.314 9.525 1DAH HZ 21 5.335 5.268 9.453 1DAH CE1 22 5.564 5.223 9.389 1DAH HE1 23 5.489 5.181 9.321 1DAH CD1 24 5.701 5.203 9.362 1DAH HD1 25 5.731 5.146 9.274 1.02033 1.02033 1.02033 I derived the topology file from PRODRG server. However the .itp file is giving only 22 atoms definition and 3 of the hydrogen atoms are missing: - DAH 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1OM 1 DAH O 1 -0.715 15.9994 2 C 1 DAH C 10.387 12.0110 3OM 1 DAH OXT 1 -0.716 15.9994 4 CH1 1 DAH CA 10.178 13.0190 5NL 1 DAH N 10.683 14.0067 6 H 1 DAH H2 10.010 1.0080 7 H 1 DAH H3 10.010 1.0080 8 H 1 DAH H1 10.011 1.0080 9 CH2 1 DAH CB 10.152 14.0270 10 C 1 DAH CG 2 -0.020 12.0110 11 CR1 1 DAH CD2 20.001 12.0110 12HC 1 DAH HD2 20.019 1.0080 13 C 1 DAH CE2 30.130 12.0110 14OA 1 DAH OE2 3 -0.197 15.9994 15 H 1 DAH HE2 30.051 1.0080 16 C 1 DAH CZ 30.130 12.0110 17OA 1 DAH OZ 3 -0.197 15.9994 18 H 1 DAH HZ 30.051 1.0080 19 CR1 1 DAH CE1 30.001 12.0110 20HC 1 DAH HE1 30.031 1.0080 21 CR1 1 DAH CD1 40.000 12.0110 22HC 1 DAH HD1 40.000 1.0080 [ bonds ] So you can see that
Re: [gmx-users] Hydrogens missing during parameterization
Anirban Ghosh wrote: Hi XAvier, Thanks for the reply. Actually I want to use this ligand with a protein and run the complex using ffG43a2 force-field of GROMACS4.0.7. So is it correct to leave away those 3 hydrogens HA, HB1 and HB2, which are not explicitly described? Because in protein-ligand complexes, hydrogen bond formations between the ligand and the protein are important? So should I continue with this .itp file with 3 less hydrogens? Thanks again. Consider basic biochemistry - do hydrogen bonds involving C-H bonds usually form? I would strongly recommend reading the primary literature for the GROMOS96 force fields, as well as any other material regarding united-atom force fields you can find. It sounds like you need a bit more fundamental understanding of what's going on. Besides, I wouldn't use that topology anyway. As I continually advise on this list, a PRODRG output is more often than not (read: basically always!) incorrect in some fashion. L-DOPA should be derived from tyrosine, therefore it is a reasonable assumption to think that its parameters should somewhat resemble this amino acid. Look at the topology - each of your C-H bonds in the aromatic ring has different charges, which certainly is not right! You should at least have functional group consistency. Before you waste your time doing a simulation with bogus parameters, you will have to consider parameterization (an advanced topic, indeed): http://www.gromacs.org/Documentation/How-tos/Parameterization In general, functional groups within GROMOS96 are very transferrable between different molecules (from personal experience), but you still have to demonstrate that your system is sound to reviewers. I know if I ever got a paper that just said we used PRODRG I would immediately want to see the parameters and know the justification for using them. -Justin Regards, Anirban On Wed, Apr 14, 2010 at 3:50 PM, XAvier Periole x.peri...@rug.nl mailto:x.peri...@rug.nl wrote: You have the proper itp file for the GROMOS FF. Some H are not explicitly described! On Apr 14, 2010, at 12:05 PM, Anirban Ghosh wrote: Hi, XAvier, Sorry for that mistake. Yes, exactly PRODRG is not giving the non-polar hydrogens. There I am using the GROMOS96.1 FF. So is there any way to get the proper .itp file? I mean any other online server like PRODRG? Or How can I derive the proper .itp file manually? Any suggestion is welcome. Thanks a lot for the prompt reply. Regards, Anirban On Wed, Apr 14, 2010 at 3:25 PM, XAvier Periole x.peri...@rug.nl mailto:x.peri...@rug.nl wrote: You are missing HB1 and HB2, not HB2 and HB3 :)) This is due to the force field our are using. Gromos I presume: it uses the united H idea: non-polar H are not explicitly modeled. you should be able to erase those from your gro file, but I would suggest you get into some literature about the FF you use. XAvier. On Apr 14, 2010, at 11:36 AM, Anirban Ghosh wrote: Hi ALL, I have a ligand LDOPA with 25 atoms (including all hydrogens).: --- DAH COORDS 25 1DAH O1 5.988 5.216 9.128 1DAH C2 5.980 5.110 9.194 1DAH OXT 3 5.951 4.985 9.139 1DAH CA 4 6.001 5.107 9.349 1DAH HA 5 5.935 5.027 9.384 1DAH N6 6.140 5.064 9.387 1DAH H2 7 6.161 4.977 9.343 1DAH H3 8 6.137 5.056 9.486 1DAH H1 9 6.206 5.133 9.356 1DAH CB 10 5.952 5.236 9.422 1DAH HB1 11 5.985 5.320 9.362 1DAH HB2 12 5.999 5.231 9.520 1DAH CG 13 5.802 5.258 9.450 1DAH CD2 14 5.761 5.333 9.565 1DAH HD2 15 5.836 5.375 9.632 1DAH CE2 16 5.623 5.353 9.592 1DAH OE2 17 5.589 5.425 9.704 1DAH HE2 18 5.672 5.454 9.752 1DAH CZ 19 5.523 5.297 9.503 1DAH OZ 20 5.387 5.314 9.525 1DAH HZ 21 5.335 5.268 9.453 1DAH CE1 22 5.564 5.223 9.389 1DAH HE1 23 5.489 5.181 9.321 1DAH CD1 24 5.701 5.203 9.362 1DAH HD1 25 5.731 5.146 9.274 1.02033 1.02033 1.02033
Re: [gmx-users] Hydrogens missing during parameterization
Well, ffG43a2 is a GROMOS FF too! So look at the topology and you'll see that it also misses some NON_POLAR hydrogens. You probably generated you itp file using pdb2gmx and got a gro file with it. Then the absence of H did not appear! The H that are involved in H-bonding are explicitly represented in GROMOS FF. The ones that are united are the NON-POLAR ones, typically in CH3/CH2 and CH groups! Check the ffG43a2.rtp file, it contains residues topologies ... Again I would suggest you get into some literature before going on. One day reading some papers on the GROMOS FF would be instructive :)) XAvier. On Apr 14, 2010, at 12:28 PM, Anirban Ghosh wrote: Hi XAvier, Thanks for the reply. Actually I want to use this ligand with a protein and run the complex using ffG43a2 force-field of GROMACS4.0.7. So is it correct to leave away those 3 hydrogens HA, HB1 and HB2, which are not explicitly described? Because in protein- ligand complexes, hydrogen bond formations between the ligand and the protein are important? So should I continue with this .itp file with 3 less hydrogens? Thanks again. Regards, Anirban On Wed, Apr 14, 2010 at 3:50 PM, XAvier Periole x.peri...@rug.nl wrote: You have the proper itp file for the GROMOS FF. Some H are not explicitly described! On Apr 14, 2010, at 12:05 PM, Anirban Ghosh wrote: Hi, XAvier, Sorry for that mistake. Yes, exactly PRODRG is not giving the non- polar hydrogens. There I am using the GROMOS96.1 FF. So is there any way to get the proper .itp file? I mean any other online server like PRODRG? Or How can I derive the proper .itp file manually? Any suggestion is welcome. Thanks a lot for the prompt reply. Regards, Anirban On Wed, Apr 14, 2010 at 3:25 PM, XAvier Periole x.peri...@rug.nl wrote: You are missing HB1 and HB2, not HB2 and HB3 :)) This is due to the force field our are using. Gromos I presume: it uses the united H idea: non-polar H are not explicitly modeled. you should be able to erase those from your gro file, but I would suggest you get into some literature about the FF you use. XAvier. On Apr 14, 2010, at 11:36 AM, Anirban Ghosh wrote: Hi ALL, I have a ligand LDOPA with 25 atoms (including all hydrogens).: --- DAH COORDS 25 1DAH O1 5.988 5.216 9.128 1DAH C2 5.980 5.110 9.194 1DAH OXT 3 5.951 4.985 9.139 1DAH CA 4 6.001 5.107 9.349 1DAH HA 5 5.935 5.027 9.384 1DAH N6 6.140 5.064 9.387 1DAH H2 7 6.161 4.977 9.343 1DAH H3 8 6.137 5.056 9.486 1DAH H1 9 6.206 5.133 9.356 1DAH CB 10 5.952 5.236 9.422 1DAH HB1 11 5.985 5.320 9.362 1DAH HB2 12 5.999 5.231 9.520 1DAH CG 13 5.802 5.258 9.450 1DAH CD2 14 5.761 5.333 9.565 1DAH HD2 15 5.836 5.375 9.632 1DAH CE2 16 5.623 5.353 9.592 1DAH OE2 17 5.589 5.425 9.704 1DAH HE2 18 5.672 5.454 9.752 1DAH CZ 19 5.523 5.297 9.503 1DAH OZ 20 5.387 5.314 9.525 1DAH HZ 21 5.335 5.268 9.453 1DAH CE1 22 5.564 5.223 9.389 1DAH HE1 23 5.489 5.181 9.321 1DAH CD1 24 5.701 5.203 9.362 1DAH HD1 25 5.731 5.146 9.274 1.02033 1.02033 1.02033 I derived the topology file from PRODRG server. However the .itp file is giving only 22 atoms definition and 3 of the hydrogen atoms are missing: - DAH 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1OM 1 DAH O 1 -0.715 15.9994 2 C 1 DAH C 10.387 12.0110 3OM 1 DAH OXT 1 -0.716 15.9994 4 CH1 1 DAH CA 10.178 13.0190 5NL 1 DAH N 10.683 14.0067 6 H 1 DAH H2 10.010 1.0080 7 H 1 DAH H3 10.010 1.0080 8 H 1 DAH H1 10.011 1.0080 9 CH2 1 DAH CB 10.152 14.0270 10 C 1 DAH CG 2 -0.020 12.0110 11 CR1 1 DAH CD2 20.001 12.0110 12HC 1 DAH HD2 20.019 1.0080 13 C 1 DAH CE2 30.130 12.0110 14OA 1 DAH OE2 3 -0.197 15.9994 15 H 1 DAH HE2
[gmx-users] *.xtc file is not getting created by mdrun program :(
hi there i tried to run MD and i wanted to use *.xtc file in vmd to visualize the protein but unfortunately there is no such file i given the command like this mdrun -nice 0 -v -s input3.tpr -o md_traj.trr -x md_traj.xtc -c md_final.gro -e md_ener.edr as procedure this should create md_traj.xtc file rite. so please can u help me out of this mesh... -- Bharath.K.Chakravarthi Ph:9535629260 -- 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] *.xtc file is not getting created by mdrun program :(
Bharath.K. Chakravarthi wrote: hi there i tried to run MD and i wanted to use *.xtc file in vmd to visualize the protein but unfortunately there is no such file i given the command like this mdrun -nice 0 -v -s input3.tpr -o md_traj.trr -x md_traj.xtc -c md_final.gro -e md_ener.edr as procedure this should create md_traj.xtc file rite. Provided that you have set nstxtcout 0 in the .mdp file. The default is 0 (no .xtc file). Consult the manual for appropriate settings. -Justin so please can u help me out of this mesh... -- Bharath.K.Chakravarthi Ph:9535629260 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] *.xtc file is not getting created by mdrun program :(
On Wed, Apr 14, 2010 at 5:31 AM, Bharath.K. Chakravarthi bharath.chakravar...@gmail.com wrote: Thank you for your kind replay sir sir in my .mdp file there is nstxtout instead of nstxtcout sir and it is set to 500 is this what u told... i have also attached the .mdp file in this mail sir On Wed, Apr 14, 2010 at 5:18 AM, Justin A. Lemkul jalem...@vt.edu wrote: Bharath.K. Chakravarthi wrote: hi there i tried to run MD and i wanted to use *.xtc file in vmd to visualize the protein but unfortunately there is no such file i given the command like this mdrun -nice 0 -v -s input3.tpr -o md_traj.trr -x md_traj.xtc -c md_final.gro -e md_ener.edr as procedure this should create md_traj.xtc file rite. Provided that you have set nstxtcout 0 in the .mdp file. The default is 0 (no .xtc file). Consult the manual for appropriate settings. -Justin so please can u help me out of this mesh... -- Bharath.K.Chakravarthi Ph:9535629260 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 -- Bharath.K.Chakravarthi Ph:9535629260 -- Bharath.K.Chakravarthi Ph:9535629260 md.mdp Description: Binary data -- 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] *.xtc file is not getting created by mdrun program :(
Thank you for your kind replay sir sir in my .mdp file there is nstxtout instead of nstxtcout sir and it is set to 500 is this what u told... i have also attached the .mdp file in this mail sir On Wed, Apr 14, 2010 at 5:18 AM, Justin A. Lemkul jalem...@vt.edu wrote: Bharath.K. Chakravarthi wrote: hi there i tried to run MD and i wanted to use *.xtc file in vmd to visualize the protein but unfortunately there is no such file i given the command like this mdrun -nice 0 -v -s input3.tpr -o md_traj.trr -x md_traj.xtc -c md_final.gro -e md_ener.edr as procedure this should create md_traj.xtc file rite. Provided that you have set nstxtcout 0 in the .mdp file. The default is 0 (no .xtc file). Consult the manual for appropriate settings. -Justin so please can u help me out of this mesh... -- Bharath.K.Chakravarthi Ph:9535629260 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 -- Bharath.K.Chakravarthi Ph:9535629260 -- 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] *.xtc file is not getting created by mdrun program :(
Bharath.K. Chakravarthi wrote: Thank you for your kind replay sir sir in my .mdp file there is nstxtout instead of nstxtcout sir and it is set to 500 is this what u told... No, this is not what I said. These are different settings entirely. nstxout is for the .trr file, nstxtcout is for the .xtc file. As I said, please consult the manual for appropriate settings. -Justin i have also attached the .mdp file in this mail sir On Wed, Apr 14, 2010 at 5:18 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Bharath.K. Chakravarthi wrote: hi there i tried to run MD and i wanted to use *.xtc file in vmd to visualize the protein but unfortunately there is no such file i given the command like this mdrun -nice 0 -v -s input3.tpr -o md_traj.trr -x md_traj.xtc -c md_final.gro -e md_ener.edr as procedure this should create md_traj.xtc file rite. Provided that you have set nstxtcout 0 in the .mdp file. The default is 0 (no .xtc file). Consult the manual for appropriate settings. -Justin so please can u help me out of this mesh... -- Bharath.K.Chakravarthi Ph:9535629260 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto: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...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Bharath.K.Chakravarthi Ph:9535629260 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] *.xtc file is not getting created by mdrun program :(
sir should i set dat to 0 or what to do On Wed, Apr 14, 2010 at 5:32 AM, Bharath.K. Chakravarthi bharath.chakravar...@gmail.com wrote: On Wed, Apr 14, 2010 at 5:31 AM, Bharath.K. Chakravarthi bharath.chakravar...@gmail.com wrote: Thank you for your kind replay sir sir in my .mdp file there is nstxtout instead of nstxtcout sir and it is set to 500 is this what u told... i have also attached the .mdp file in this mail sir On Wed, Apr 14, 2010 at 5:18 AM, Justin A. Lemkul jalem...@vt.eduwrote: Bharath.K. Chakravarthi wrote: hi there i tried to run MD and i wanted to use *.xtc file in vmd to visualize the protein but unfortunately there is no such file i given the command like this mdrun -nice 0 -v -s input3.tpr -o md_traj.trr -x md_traj.xtc -c md_final.gro -e md_ener.edr as procedure this should create md_traj.xtc file rite. Provided that you have set nstxtcout 0 in the .mdp file. The default is 0 (no .xtc file). Consult the manual for appropriate settings. -Justin so please can u help me out of this mesh... -- Bharath.K.Chakravarthi Ph:9535629260 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 -- Bharath.K.Chakravarthi Ph:9535629260 -- Bharath.K.Chakravarthi Ph:9535629260 -- Bharath.K.Chakravarthi Ph:9535629260 -- 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] *.xtc file is not getting created by mdrun program :(
Bharath.K. Chakravarthi wrote: sir should i set dat to 0 or what to do I clearly stated that you should set nstxtcout 0 in my first message. Leaving any output control parameter set to zero means produce output every zero steps or essentially, not at all. -Justin On Wed, Apr 14, 2010 at 5:32 AM, Bharath.K. Chakravarthi bharath.chakravar...@gmail.com mailto:bharath.chakravar...@gmail.com wrote: On Wed, Apr 14, 2010 at 5:31 AM, Bharath.K. Chakravarthi bharath.chakravar...@gmail.com mailto:bharath.chakravar...@gmail.com wrote: Thank you for your kind replay sir sir in my .mdp file there is nstxtout instead of nstxtcout sir and it is set to 500 is this what u told... i have also attached the .mdp file in this mail sir On Wed, Apr 14, 2010 at 5:18 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Bharath.K. Chakravarthi wrote: hi there i tried to run MD and i wanted to use *.xtc file in vmd to visualize the protein but unfortunately there is no such file i given the command like this mdrun -nice 0 -v -s input3.tpr -o md_traj.trr -x md_traj.xtc -c md_final.gro -e md_ener.edr as procedure this should create md_traj.xtc file rite. Provided that you have set nstxtcout 0 in the .mdp file. The default is 0 (no .xtc file). Consult the manual for appropriate settings. -Justin so please can u help me out of this mesh... -- Bharath.K.Chakravarthi Ph:9535629260 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto: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...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Bharath.K.Chakravarthi Ph:9535629260 -- Bharath.K.Chakravarthi Ph:9535629260 -- Bharath.K.Chakravarthi Ph:9535629260 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] *.xtc file is not getting created by mdrun program :(
Thank you very much for your replay sir... On Wed, Apr 14, 2010 at 5:36 AM, Justin A. Lemkul jalem...@vt.edu wrote: Bharath.K. Chakravarthi wrote: sir should i set dat to 0 or what to do I clearly stated that you should set nstxtcout 0 in my first message. Leaving any output control parameter set to zero means produce output every zero steps or essentially, not at all. -Justin On Wed, Apr 14, 2010 at 5:32 AM, Bharath.K. Chakravarthi bharath.chakravar...@gmail.com mailto:bharath.chakravar...@gmail.com wrote: On Wed, Apr 14, 2010 at 5:31 AM, Bharath.K. Chakravarthi bharath.chakravar...@gmail.com mailto:bharath.chakravar...@gmail.com wrote: Thank you for your kind replay sir sir in my .mdp file there is nstxtout instead of nstxtcout sir and it is set to 500 is this what u told... i have also attached the .mdp file in this mail sir On Wed, Apr 14, 2010 at 5:18 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Bharath.K. Chakravarthi wrote: hi there i tried to run MD and i wanted to use *.xtc file in vmd to visualize the protein but unfortunately there is no such file i given the command like this mdrun -nice 0 -v -s input3.tpr -o md_traj.trr -x md_traj.xtc -c md_final.gro -e md_ener.edr as procedure this should create md_traj.xtc file rite. Provided that you have set nstxtcout 0 in the .mdp file. The default is 0 (no .xtc file). Consult the manual for appropriate settings. -Justin so please can u help me out of this mesh... -- Bharath.K.Chakravarthi Ph:9535629260 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto: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...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Bharath.K.Chakravarthi Ph:9535629260 -- Bharath.K.Chakravarthi Ph:9535629260 -- Bharath.K.Chakravarthi Ph:9535629260 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 -- Bharath.K.Chakravarthi Ph:9535629260 -- 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] nstfout parameter
hi .. in my *.mdp file one parameter named mstfout is set to 0 can you please tell me the use of this parameter -- Bharath.K.Chakravarthi Ph:9535629260 -- 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] nstfout parameter
Bharath.K. Chakravarthi wrote: hi .. in my *.mdp file one parameter named mstfout is set to 0 can you please tell me the use of this parameter Please see the manual, section 7.3.8. -Justin -- Bharath.K.Chakravarthi Ph:9535629260 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] How to set the density of the box?
nbsp;nbsp;nbsp;nbsp;nbsp; Hello, I want to set the density of the box (e.g. set 1 g/ml for the water box). I use the density option in the editconf, then use the genbox to generate the box, but the result of the density is not what I setted. How cannbsp; I do ? nbsp;nbsp;nbsp;nbsp;nbsp; I have another question, I don't find the tip3p.gro and spce.gro water modelnbsp; in the top file, only have the .itp document. if I want to generate the TIP3P water box, how can I do, ornbsp; where can I get the tip3p.gro and spce.gro documents? nbsp;nbsp;nbsp;nbsp;nbsp; Thank you !-- 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] How to set the density of the box?
kecy...@sina.com wrote: Hello, I want to set the density of the box (e.g. set 1 g/ml for the water box). I use the density option in the editconf, then use the genbox to generate the box, but the result of the density is not what I setted. How can I do ? The density of the box will be governed by how accurate the water model is in reproducing experimental values. As far as I know, there isn't a water model that gets density dead on. You could alter the box dimensions manually and use a constant-volume ensemble, but whether or not it's appropriate to make such a modification is questionable, since the water models are designed to reproduce certain values with certain accuracy. I have another question, I don't find the tip3p.gro and spce.gro water model in the top file, only have the .itp document. if I want to generate the TIP3P water box, how can I do, or where can I get the tip3p.gro and spce.gro documents? You don't need anything special, just coordinates for a 3-point water model and sufficient equilibration: http://www.gromacs.org/Documentation/How-tos/TIP3P_coordinate_file -Justin Thank you ! -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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] OpenMM
On 14/04/2010 7:10 PM, PACIELLO GIULIA wrote: Well, I have used the option -rerun to 'rerun' on CPU the simulation from the parallel code. As you can see in the following tables, results are very similar for non bonded terms, but not for the other energetic terms (these are avereges obtained from g_energy): You haven't done a simulation. You've done an energy minimization. There's no reason to expect the same result for EM on different machines because there are so many different minima that might be found, and small numerical differences might mean you find different ones. PARALLEL CODE Angle: 4256.27 Prop-di: 322.302 R-B: 3101.14 LJ-14: 2107.6 Coul-14: 15212 LJ(SR): -3410.22 Coul(SR): -29368.3 RF(excl): -9425.23 Pot.En: -17204.5 Kin.En: 5243.87 Tot.En: -11960.6 SERIAL CODE: Angle: 6089.56 Prop-di: 466.121 R-B: 3677.95 LJ-14: 2234.85 Coul-14: 15149.8 LJ(SR): -3144 Coul(SR): -29240.7 RF(excl): -9425.25 Pot.En: -14191.7 Kin.En: 8262.96 Tot.En: -5929.78 I can't use the -reprod option, but I have noticed that the .gro files after the energy minimization are very similar (I have performed this minimization on the .gro files obtained running the parallel and serial codes)...systems are converging to the same equilibrium ensamble? No, they've just done an EM. There's no velocities yet, so they're not in any ensemble. Equilibrate, and then look at ensemble averages of the equilibrated systems. Mark -- 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] Concerns with g_wham
Hello, I have been using g_wham, but I have a few questions that I can't find answers to online. When using WHAM, one does not need the forces between the pull groups to calculate the PMF, yet g_wham won't run without it. Is there a reason for this? Also, when using the pull code, I am allowed to define the spring constant K for umbrella sampling, but I do not designate where the umbrella potential is centered. How does gromacs determine this? I am interested as I would like to create a PMF using umbrella integration (from code I will write myself) rather than use WHAM. To do this and still use the umbrella sampling runs used with GROMACS, I need to know where my umbrella potentials are centered. Thank you, Jennifer -- 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] how to calculate diffusion constant of the entire lipid-bilayer
Hi, I was interested in calculating the diffusion constant of the center of mass of entire lipid-bilayer ( not individual lipid molecules). Regarding this, I had two doubts I wanted to clarify: 1. Since I am interested in calculating the diffusion constant of the bilayer iteself, I guess I should allow the drift of the bilayer and hence not then remove the center of mass motion of bilayer (and solvent ) separately. Is that right ? If so, is it still OK to remove the center of mass of whole system ( bilayer + water together ) ? 2. How to calculate the mean square displacement of center of mass of the entire bilayer. I guess, g_msd program by default, calculate the diffusion constant of the individual atoms or molecules.But, is there a way to get the diffusion constant of the entire bilayer center of mass ? If I specify the index group which consist of all the atoms of the bilayer, will g_msd provide the diffusion constant of its center of mass or it will give the diffusion constant of individual atoms ? I guess, in that case, one should not use -rmcomm option . Is that right ? Thanks Jagannath -- 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] modifying source code
Hello all, I am trying to modify the source code. My simulation system consists of several huge modecules disolved in a liquid. The relative orientation among the huge molecules is not significant in the system, and I concern structural properties only, not dynamic properties, in the equilibrium state. I guess it'll take very long time to equilibrate this because it's a huge system. So here's an idea. I sum all the forces exerted on a huge molecule and move the center of mass of it translationally only without rotation, so I can save the computation time. To do this, I have to change the source code. So, I read mdrun.c and several source code files, but I could hardly understand them. When I used dlpoly, the reference manual helped me a lot understand the source code. It has explanations on all the variables and subroutines, but I can't find one for gromacs. I guess it's hard to answer my question and to make me understand the source code through email. If there exists such a manual on the source, please let me know how to get it. Thank you in advance. Sang-Won. --- Sang-Won Park Ph. D. student Department of Chemistry Seoul National University Seoul, Korea 151-747 Tel: 822-880-4369 -- 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] modifying source code
On 15/04/2010 12:32 PM, Sang-Won Park wrote: Hello all, I am trying to modify the source code. My simulation system consists of several huge modecules disolved in a liquid. The relative orientation among the huge molecules is not significant in the system, and I concern structural properties only, not dynamic properties, in the equilibrium state. I guess it'll take very long time to equilibrate this because it's a huge system. So here's an idea. I sum all the forces exerted on a huge molecule and move the center of mass of it translationally only without rotation, so I can save the computation time. I don't see why this would give you a valid ensemble, or save computation time. You still need to evaluate every force and move every atom - you're just adding in an intermediate step that would slow things down a lot. To do this, I have to change the source code. So, I read mdrun.c and several source code files, but I could hardly understand them. When I used dlpoly, the reference manual helped me a lot understand the source code. It has explanations on all the variables and subroutines, but I can't find one for gromacs. I guess it's hard to answer my question and to make me understand the source code through email. If there exists such a manual on the source, please let me know how to get it. Thank you in advance. There's a mixture of stuff available here http://www.gromacs.org/Developer_Zone/Programming_Guide but it may or may not suit your purposes. Mark -- 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
