[gmx-users] About free enrgy calculation
Thank you for your previous reply Sorry In previous Mail i wrongly stated that decoupling CNT ( as you stated it is big Molecule ) To do free energy calculation based on on your tutorial 6( methane/water) I want to decouple Water from CNT which is Wrapped by assembly of Cyclic peptide (the stability of assembly is mainly due to Vandewall's interaction between CNT and cyclic peptide) When I Fix following parameter for My system in mdp files free_energy = yes init-lambda = 0.00 delta_lambda = 0.00 sc-alpha = 1 sc-power = 2.0 sc-sigma = 0.3 It show follwin Notes How to Avoid this? NOTE 1 [file /usr/local/gromacs4.6.11single/bin/MDP/em_steep_0.mdp]: With PME there is a minor soft core effect present at the cut-off, proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on energy conservation, but usually other effects dominate. With a common sigma value of 0.34 nm the fraction of the particle-particle potential at the cut-off at lambda=0.5 is around 2.4e-04, while ewald-rtol is 1.0e-05. May i extend your tutorial parameter to my system ? because you also Decouple water from Metahne . Or is ther is Any Thump rule with regards S.Vidhyasankar -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] MD for extracellular and transmembrane system
Dear all Gromacs user, I am knew to Gromacs for molecular dynamics. One off the hurdle I encountered is that can I use GROMACS for modelling protein with extracellular and transmembrane domain i.e., maintain water/lipid system in molecular dynamics simulation. Can I add the water system for extracellular domain and lipid system for transmembrane domain in GROMACS? if yes please provide necessary information. -- - Rahul Dhakne Research Scholar, NIPER (Mohali). in.linkedin.com/in/rahul777/ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] g_dielectric errors for getting frequency dependent dielectric constants
Dear all, I have some questions when calculating frequency dependent dielectric constants throughg_dielectric. 1. After using g_dipoles -corr mol command to get the dipcorr.xvg, if I uesd g_dielectric program, the error is as following. Fatal error: nparm = 0 in file expfit.c, line 465 if I used g_dielectric -eint 50 -bfit 5 -efit 100 -ffn exp , then the error is: nbegin = 50, x[nbegin] = 5, tbegin = 5 Step chi^2 Lambda A1 A2 A3 Segmentation Fault 2. When I read the manul aboutg_dielectric, I have a question about the output file epsw.xvg . In the manul, it discribs The second file contains the real and imaginary parts of the frequency-dependent dielectric constant . How can I get the real parts of the frequency-dependent dielectric constant only ? I appreciate your help. Thanks a lot! -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] About free enrgy calculation
On 6/1/14, 3:30 AM, vidhya sankar wrote: Thank you for your previous reply Sorry In previous Mail i wrongly stated that decoupling CNT ( as you stated it is big Molecule ) To do free energy calculation based on on your tutorial 6( methane/water) I want to decouple Water from CNT which is Wrapped by assembly of Cyclic peptide (the stability of assembly is mainly due to Vandewall's interaction between CNT and cyclic peptide) Decoupling water from the system will likely be highly unstable and I'm not sure what use the value is, if the simulations even run. When I Fix following parameter for My systemin mdp files free_energy = yes init-lambda = 0.00 delta_lambda = 0.00 sc-alpha = 1 sc-power = 2.0 The values of sc-alpha and sc-power are unusual. I stick by my recommendation to use the same settings as in my tutorial. sc-sigma = 0.3 It show follwin Notes How to Avoid this? NOTE 1 [file /usr/local/gromacs4.6.11single/bin/MDP/em_steep_0.mdp]: With PME there is a minor soft core effect present at the cut-off, proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on energy conservation, but usually other effects dominate. With a common sigma value of 0.34 nm the fraction of the particle-particle potential at the cut-off at lambda=0.5 is around 2.4e-04, while ewald-rtol is 1.0e-05. May i extend your tutorial parameter to my system ? because you also Decouple water from Metahne . Or is ther is Any Thump rule No, I don't decouple water from methane, I do the opposite. The water interactions remain the same at all lambda values. The methane molecule is decoupled to calculate the free energy of hydration. I don't get a clear sense of what you're even trying to calculate in your system. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] MD for extracellular and transmembrane system
On 6/1/14, 3:51 AM, rahul dhakne wrote: Dear all Gromacs user, I am knew to Gromacs for molecular dynamics. One off the hurdle I encountered is that can I use GROMACS for modelling protein with extracellular and transmembrane domain i.e., maintain water/lipid system in molecular dynamics simulation. Can I add the water system for extracellular domain and lipid system for transmembrane domain in GROMACS? if yes please provide necessary information. http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html Choose a force field carefully. There are many options. The tutorial illustrates on simple approach, but there are other parameter sets that may be more suitable, depending on your system. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] help needed
Dear All, I am testing my gromacs code using user-specified potential functions (LJ as well as Buckingham as non-bonded potentials). *Minimization run with these potentials runs fine*. However, equilibration run gives following error at which I am clueless. Could anyone help? Is it because total charge is -0.018 and not zero? ... Non-default thread affinity set probably by the OpenMP library, disabling internal thread affinity starting mdrun 'tio2_formate' 100 steps, 1000.0 ps. [c418-701.stampede.tacc.utexas.edu:mpi_rank_5][error_sighandler] Caught error: Segmentation fault (signal 11) [c418-701.stampede.tacc.utexas.edu:mpispawn_0][readline] Unexpected End-Of-File on file descriptor 7. MPI process died? [c418-701.stampede.tacc.utexas.edu:mpispawn_0][mtpmi_processops] Error while reading PMI socket. MPI process died? [c418-701.stampede.tacc.utexas.edu:mpispawn_0][child_handler] MPI process (rank: 5, pid: 122921) terminated with signal 11 - abort job [c418-701.stampede.tacc.utexas.edu:mpirun_rsh][process_mpispawn_connection] mpispawn_0 from node c418-701 aborted: Error while reading a PMI socket (4) [c428-301.stampede.tacc.utexas.edu:mpispawn_1][read_size] Unexpected End-Of-File on file descriptor 21. MPI process died? [c428-301.stampede.tacc.utexas.edu:mpispawn_1][read_size] Unexpected End-Of-File on file descriptor 21. MPI process died? [c428-301.stampede.tacc.utexas.edu:mpispawn_1][handle_mt_peer] Error while reading PMI socket. MPI process died? [c428-902.stampede.tacc.utexas.edu:mpispawn_2][read_size] Unexpected End-Of-File on file descriptor 21. MPI process died? [c428-902.stampede.tacc.utexas.edu:mpispawn_2][read_size] Unexpected End-Of-File on file descriptor 21. MPI process died? [c428-902.stampede.tacc.utexas.edu:mpispawn_2][handle_mt_peer] Error while reading PMI socket. MPI process died? TACC: MPI job exited with code: 1 TACC: Shutdown complete. Exiting. NOTE 1 [file lnanopf3.top, line 4422]: System has non-zero total charge: -0.018000 Total charge should normally be an integer. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic for discussion on how close it should be to an integer. --- Program grompp, VERSION 4.6.5 Source code file: /work/01906/xzhu216/gromacs/source/gromacs-4.6.5/src/gmxlib/futil.c, line: 593 File input/output error: /work/01019/cmahajan/postdoc/mapotruns/r1/eq/lnanop.gro ... Thanks a lot! regards Chetan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] help needed
More information: As the log file shows, coulomb interaction energy is shooting to nan during equilibration where error occurs. Coulomb interaction energy during minimization is finite. Thanks Chetan On Sun, Jun 1, 2014 at 4:44 PM, Chetan Mahajan chetanv...@gmail.com wrote: Dear All, I am testing my gromacs code using user-specified potential functions (LJ as well as Buckingham as non-bonded potentials). *Minimization run with these potentials runs fine*. However, equilibration run gives following error at which I am clueless. Could anyone help? Is it because total charge is -0.018 and not zero? ... Non-default thread affinity set probably by the OpenMP library, disabling internal thread affinity starting mdrun 'tio2_formate' 100 steps, 1000.0 ps. [c418-701.stampede.tacc.utexas.edu:mpi_rank_5][error_sighandler] Caught error: Segmentation fault (signal 11) [c418-701.stampede.tacc.utexas.edu:mpispawn_0][readline] Unexpected End-Of-File on file descriptor 7. MPI process died? [c418-701.stampede.tacc.utexas.edu:mpispawn_0][mtpmi_processops] Error while reading PMI socket. MPI process died? [c418-701.stampede.tacc.utexas.edu:mpispawn_0][child_handler] MPI process (rank: 5, pid: 122921) terminated with signal 11 - abort job [c418-701.stampede.tacc.utexas.edu:mpirun_rsh][process_mpispawn_connection] mpispawn_0 from node c418-701 aborted: Error while reading a PMI socket (4) [c428-301.stampede.tacc.utexas.edu:mpispawn_1][read_size] Unexpected End-Of-File on file descriptor 21. MPI process died? [c428-301.stampede.tacc.utexas.edu:mpispawn_1][read_size] Unexpected End-Of-File on file descriptor 21. MPI process died? [c428-301.stampede.tacc.utexas.edu:mpispawn_1][handle_mt_peer] Error while reading PMI socket. MPI process died? [c428-902.stampede.tacc.utexas.edu:mpispawn_2][read_size] Unexpected End-Of-File on file descriptor 21. MPI process died? [c428-902.stampede.tacc.utexas.edu:mpispawn_2][read_size] Unexpected End-Of-File on file descriptor 21. MPI process died? [c428-902.stampede.tacc.utexas.edu:mpispawn_2][handle_mt_peer] Error while reading PMI socket. MPI process died? TACC: MPI job exited with code: 1 TACC: Shutdown complete. Exiting. NOTE 1 [file lnanopf3.top, line 4422]: System has non-zero total charge: -0.018000 Total charge should normally be an integer. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic for discussion on how close it should be to an integer. --- Program grompp, VERSION 4.6.5 Source code file: /work/01906/xzhu216/gromacs/source/gromacs-4.6.5/src/gmxlib/futil.c, line: 593 File input/output error: /work/01019/cmahajan/postdoc/mapotruns/r1/eq/lnanop.gro ... Thanks a lot! regards Chetan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] help needed
Hi, What's the smallest relevant neutral system you can think of? Test your implementation of your model on that, on a local machine, not a supercomputer ;-) If there's any diagnosis of why the crash happens, it will be in the log file. But you seem like you have far too many variables to know where the major problem lies. Mark On Sun, Jun 1, 2014 at 11:55 PM, Chetan Mahajan chetanv...@gmail.com wrote: More information: As the log file shows, coulomb interaction energy is shooting to nan during equilibration where error occurs. Coulomb interaction energy during minimization is finite. Thanks Chetan On Sun, Jun 1, 2014 at 4:44 PM, Chetan Mahajan chetanv...@gmail.com wrote: Dear All, I am testing my gromacs code using user-specified potential functions (LJ as well as Buckingham as non-bonded potentials). *Minimization run with these potentials runs fine*. However, equilibration run gives following error at which I am clueless. Could anyone help? Is it because total charge is -0.018 and not zero? ... Non-default thread affinity set probably by the OpenMP library, disabling internal thread affinity starting mdrun 'tio2_formate' 100 steps, 1000.0 ps. [c418-701.stampede.tacc.utexas.edu:mpi_rank_5][error_sighandler] Caught error: Segmentation fault (signal 11) [c418-701.stampede.tacc.utexas.edu:mpispawn_0][readline] Unexpected End-Of-File on file descriptor 7. MPI process died? [c418-701.stampede.tacc.utexas.edu:mpispawn_0][mtpmi_processops] Error while reading PMI socket. MPI process died? [c418-701.stampede.tacc.utexas.edu:mpispawn_0][child_handler] MPI process (rank: 5, pid: 122921) terminated with signal 11 - abort job [c418-701.stampede.tacc.utexas.edu: mpirun_rsh][process_mpispawn_connection] mpispawn_0 from node c418-701 aborted: Error while reading a PMI socket (4) [c428-301.stampede.tacc.utexas.edu:mpispawn_1][read_size] Unexpected End-Of-File on file descriptor 21. MPI process died? [c428-301.stampede.tacc.utexas.edu:mpispawn_1][read_size] Unexpected End-Of-File on file descriptor 21. MPI process died? [c428-301.stampede.tacc.utexas.edu:mpispawn_1][handle_mt_peer] Error while reading PMI socket. MPI process died? [c428-902.stampede.tacc.utexas.edu:mpispawn_2][read_size] Unexpected End-Of-File on file descriptor 21. MPI process died? [c428-902.stampede.tacc.utexas.edu:mpispawn_2][read_size] Unexpected End-Of-File on file descriptor 21. MPI process died? [c428-902.stampede.tacc.utexas.edu:mpispawn_2][handle_mt_peer] Error while reading PMI socket. MPI process died? TACC: MPI job exited with code: 1 TACC: Shutdown complete. Exiting. NOTE 1 [file lnanopf3.top, line 4422]: System has non-zero total charge: -0.018000 Total charge should normally be an integer. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic for discussion on how close it should be to an integer. --- Program grompp, VERSION 4.6.5 Source code file: /work/01906/xzhu216/gromacs/source/gromacs-4.6.5/src/gmxlib/futil.c, line: 593 File input/output error: /work/01019/cmahajan/postdoc/mapotruns/r1/eq/lnanop.gro ... Thanks a lot! regards Chetan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] hydrogen bond analysis
Dear all I wish to analyze hydrogen bonds in a gromacs MD trajectories with g_hbond. I want to get information about the life time of individual hbonds between the receptor and ligand in the structure through the trajector. in the output log file of g_hbond command, I can find the list of individual hbonds. But by using what option can I get the life time of each of these hbonds? I cannot the -life option provides a list as following: 10.000 2.399e-02 2.399e-01 30.000 8.837e-03 2.651e-01 50.000 4.897e-03 2.448e-01 70.000 2.525e-03 1.767e-01 90.000 2.219e-03 1.997e-01 110.000 1.760e-03 1.936e-01 130.000 1.033e-03 1.343e-01 150.000 7.651e-04 1.148e-01...But I don't know what does these mean. Could you help me with that? Yeping Sun Institute of Microbiology, Chinese Academy of Sciences -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Simplified picture: comments invited
Hi, Unfortunately, there is no scope I can try smaller version of the system. However, let me explain one lead that I indicated earlier. Coulomb energy at the end of minimization is -5E-7, which becomes -nan at the zeroth step of NPT molecular dynamics run after minimization and thus code crashes. Question is what is it that is giving two different energy values (-5E-7 and -nan) for the same atomic configurations ( end of minimization, beginning of molecular dynamics)? I removed barostat, thermostat, h-bond constraints from the MD code, so as to come as close to minimization run as possible. However, coulomb energy in MD code is still blowing up. This is very interesting since as I said we have two points with different energy, but same atomic configuration, any further leads? (total charge is -0.018 in both minimization as well as MD code, so that's not affecting, water is flexible during minimization and not so during MD. However, that should not matter, since code is crashing very initial step of MD run). Thanks Chetan On Sun, Jun 1, 2014 at 5:11 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, What's the smallest relevant neutral system you can think of? Test your implementation of your model on that, on a local machine, not a supercomputer ;-) If there's any diagnosis of why the crash happens, it will be in the log file. But you seem like you have far too many variables to know where the major problem lies. Mark On Sun, Jun 1, 2014 at 11:55 PM, Chetan Mahajan chetanv...@gmail.com wrote: More information: As the log file shows, coulomb interaction energy is shooting to nan during equilibration where error occurs. Coulomb interaction energy during minimization is finite. Thanks Chetan On Sun, Jun 1, 2014 at 4:44 PM, Chetan Mahajan chetanv...@gmail.com wrote: Dear All, I am testing my gromacs code using user-specified potential functions (LJ as well as Buckingham as non-bonded potentials). *Minimization run with these potentials runs fine*. However, equilibration run gives following error at which I am clueless. Could anyone help? Is it because total charge is -0.018 and not zero? ... Non-default thread affinity set probably by the OpenMP library, disabling internal thread affinity starting mdrun 'tio2_formate' 100 steps, 1000.0 ps. [c418-701.stampede.tacc.utexas.edu:mpi_rank_5][error_sighandler] Caught error: Segmentation fault (signal 11) [c418-701.stampede.tacc.utexas.edu:mpispawn_0][readline] Unexpected End-Of-File on file descriptor 7. MPI process died? [c418-701.stampede.tacc.utexas.edu:mpispawn_0][mtpmi_processops] Error while reading PMI socket. MPI process died? [c418-701.stampede.tacc.utexas.edu:mpispawn_0][child_handler] MPI process (rank: 5, pid: 122921) terminated with signal 11 - abort job [c418-701.stampede.tacc.utexas.edu: mpirun_rsh][process_mpispawn_connection] mpispawn_0 from node c418-701 aborted: Error while reading a PMI socket (4) [c428-301.stampede.tacc.utexas.edu:mpispawn_1][read_size] Unexpected End-Of-File on file descriptor 21. MPI process died? [c428-301.stampede.tacc.utexas.edu:mpispawn_1][read_size] Unexpected End-Of-File on file descriptor 21. MPI process died? [c428-301.stampede.tacc.utexas.edu:mpispawn_1][handle_mt_peer] Error while reading PMI socket. MPI process died? [c428-902.stampede.tacc.utexas.edu:mpispawn_2][read_size] Unexpected End-Of-File on file descriptor 21. MPI process died? [c428-902.stampede.tacc.utexas.edu:mpispawn_2][read_size] Unexpected End-Of-File on file descriptor 21. MPI process died? [c428-902.stampede.tacc.utexas.edu:mpispawn_2][handle_mt_peer] Error while reading PMI socket. MPI process died? TACC: MPI job exited with code: 1 TACC: Shutdown complete. Exiting. NOTE 1 [file lnanopf3.top, line 4422]: System has non-zero total charge: -0.018000 Total charge should normally be an integer. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic for discussion on how close it should be to an integer. --- Program grompp, VERSION 4.6.5 Source code file: /work/01906/xzhu216/gromacs/source/gromacs-4.6.5/src/gmxlib/futil.c, line: 593 File input/output error: /work/01019/cmahajan/postdoc/mapotruns/r1/eq/lnanop.gro ... Thanks a lot! regards Chetan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at
Re: [gmx-users] Why does the list keep unsubscribing me?
Hi Administrators, I have been unsubscribed now for the third time (twice in the same month). This is getting increasingly annoying now. Can there be a fix to mailman to look for genuine email, or to send a confirmation link to unsubscribe (the same as for subscription) ? Thanks, Abhi From: xru...@live.com To: gmx-us...@gromacs.org Date: Thu, 15 May 2014 03:51:37 + Subject: Re: [gmx-users] Why does the list keep unsubscribing me? Thanks for the explanation Rossen.I hope mailman gets some more artificial intelligence in coming future :).cheers,Abhi Date: Wed, 14 May 2014 14:33:00 +0200 From: ros...@kth.se To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Why does the list keep unsubscribing me? Hi, Someone else mentioned the same recently. Automatic removal can happen if someone, e.g. a spammer, sends a mail to gmx-users-unsubscr...@gromacs.org while faking your email address in the From: field. Mailman is now maintained centrally by the university, so I can't dig in the logs for more information. Rossen On 14/05/14 10:29, X Rules wrote: This is the second time in 2 months, that I am unsubscribed from the list and i have to subscribe again. I just get an email that you have been unsubscribed from the list? How can I get unsubscribed without my intervention is beyond understanding? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Soln to visualised long molecule bonds across box in VMD
When visualising a simulation with VMD, a significant number of people encounter an issue where the bonds, typically appearing when loading a trajectory on a starting structure (in which the bonds are correct), then being drawn across the box. There are some extensive discussions on this emailing list on how to use trjconv to deal with the problem. Additionally, someone recently posted to the VMD emailing list some possible solutions and thought this might be of interest/use to people here. http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/23787.html Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
