Re: [gmx-users] snapshot
look for either -dt or -skip. Dr. Vitaly V. Chaban On Mon, Jul 15, 2013 at 2:03 AM, Rama ramkishn...@gmail.com wrote: Hi, How to get a snapshots in equal intervals of time (250ps) from production MD trajectory. I'm using -sep , -t0, -timestep but output came only one .gro file. -- View this message in context: http://gromacs.5086.x6.nabble.com/snapshot-tp5009837.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] How to calculate enthalpy
Hi I want calculate the enthalpy of water molecule corresponding to protein folded and unfolded state. How much a single water molecule (enthalpy and free energy) contribute in folding ? Can we calculate enthapy from g_energy? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] How to calculate enthalpy
Sure, you can. Dr. Vitaly V. Chaban On Mon, Jul 15, 2013 at 8:38 AM, pooja_gu...@nccs.res.in wrote: Hi I want calculate the enthalpy of water molecule corresponding to protein folded and unfolded state. How much a single water molecule (enthalpy and free energy) contribute in folding ? Can we calculate enthapy from g_energy? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] How to calculate enthalpy
On 07/15/2013 10:20 AM, Dr. Vitaly Chaban wrote: Sure, you can. Dr. Vitaly V. Chaban I've got a question for it. Why the calculated entropy is negative? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] How to calculate enthalpy
Thanks Vitaly but how?? let's say the difference between unfolded to folded protein is 100 water molecules. What is the correct procedure to calculate (theoretically) the entrapy correspond to single water molecule for stabilizing/destabilizing the protein. help me Sure, you can. Dr. Vitaly V. Chaban On Mon, Jul 15, 2013 at 8:38 AM, pooja_gu...@nccs.res.in wrote: Hi I want calculate the enthalpy of water molecule corresponding to protein folded and unfolded state. How much a single water molecule (enthalpy and free energy) contribute in folding ? Can we calculate enthapy from g_energy? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] How to calculate enthalpy
H = U +pV, all these terms are available through g_energy. Your resulting values will be per mole, so I would perform no additional normalization. Personally, I would simulate all cases (folded, unfolded, etc) with the same number of waters -- to avoid any possible artifacts. Dr. Vitaly V. Chaban On Mon, Jul 15, 2013 at 9:34 AM, pooja_gu...@nccs.res.in wrote: Thanks Vitaly but how?? let's say the difference between unfolded to folded protein is 100 water molecules. What is the correct procedure to calculate (theoretically) the entrapy correspond to single water molecule for stabilizing/destabilizing the protein. help me Sure, you can. Dr. Vitaly V. Chaban On Mon, Jul 15, 2013 at 8:38 AM, pooja_gu...@nccs.res.in wrote: Hi I want calculate the enthalpy of water molecule corresponding to protein folded and unfolded state. How much a single water molecule (enthalpy and free energy) contribute in folding ? Can we calculate enthapy from g_energy? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] enery conserving problem in NVE simulations with SMW4-NPD polarizable force field
Hello, I'm trying to simulate liquid water (512 water molecules) with SMW4-NPD polarizable force field. The NVT simulation looks fine, but when I restart it with NVE runs, the total energy of the system keeps drifting down. The time step I'm using now is 0.5 fs and emtol=0.01 kJ/mol/nm. Gromacs is also compiled with double precision. Does anyone have any suggestions for this kind of problem? Thanks a lot. Regards, Yun My .mdp file: ; RUN CONTROL PARAMETERS integrator = md tinit= 800 init_step=0 dt = 0.0005 ; time step (ps) nsteps = 40 ; number of steps ; OUTPUT CONTROL OPTIONS nstenergy= 100 nstxout =100 ; NEIGHBORSEARCHING PARAMETERS nstlist = -1 ns_type = grid pbc = xyz rlist= 1.24 ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype = PME-Switch rcoulomb = 1.05 rcoulomb_switch = 0.85 vdw-type = shift rvdw = 1.05 ewald_rtol =1e-4 ; OPTIONS FOR BONDS constraints = h-bonds ; Type of constraint algorithm constraint-algorithm = Lincs ; Polarizable model parameters emtol = 0.01 niter = 20 ; Temperature coupling tcoupl = no ; pressure coupling pcoupl= no ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = no -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] AMINOACIDS
Dear Justin I don't know how can I detect the protonation state of amino acids in specific pH. Can you help me? Thank you Fatemeh Ramezani -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] AMINOACIDS
On 7/15/13 7:56 AM, fatemeh ramezani wrote: Dear Justin I don't know how can I detect the protonation state of amino acids in specific pH. Can you help me? There are various methods for pKa calculations, and based on those results you can choose the appropriate states with pdb2gmx command-line options. Again, this topic is covered extensively in the archive and you would benefit from some of the previous discussions that I will not repeat here. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Associate 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 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Using the checkpoint file to restore corrupt trajectory.
Hi, I have a 20 ns long trajectory which has become corrupted beyond 18ns. I have the full checkpoint file. Is there any way I can use mdrun and the .cpt to rerun the simulation from 18ns and append it to the current .xtc (After I have clipped the part beyond 18ns by trjconv)? I did not find the appropriate flag in the mdrun online manual pages. Thanks. -- View this message in context: http://gromacs.5086.x6.nabble.com/Using-the-checkpoint-file-to-restore-corrupt-trajectory-tp5009851.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Using the checkpoint file to restore corrupt trajectory.
On 7/15/13 8:38 AM, Rajat Desikan wrote: Hi, I have a 20 ns long trajectory which has become corrupted beyond 18ns. I have the full checkpoint file. Is there any way I can use mdrun and the .cpt to rerun the simulation from 18ns and append it to the current .xtc (After I have clipped the part beyond 18ns by trjconv)? I did not find the appropriate flag in the mdrun online manual pages. It's no different than doing any restart. mdrun -s topol.tpr -cpi good_state.cpt -noappend Then concatenate trajectory and energy files with trjcat and eneconv. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Associate 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 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Using the checkpoint file to restore corrupt trajectory.
Hi Justin, The checkpoint file has gone on to 20 ns. If I do a rerun, the simulation will finish in one step. On Mon, Jul 15, 2013 at 6:11 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/15/13 8:38 AM, Rajat Desikan wrote: Hi, I have a 20 ns long trajectory which has become corrupted beyond 18ns. I have the full checkpoint file. Is there any way I can use mdrun and the .cpt to rerun the simulation from 18ns and append it to the current .xtc (After I have clipped the part beyond 18ns by trjconv)? I did not find the appropriate flag in the mdrun online manual pages. It's no different than doing any restart. mdrun -s topol.tpr -cpi good_state.cpt -noappend Then concatenate trajectory and energy files with trjcat and eneconv. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Associate Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Fw: [gmx-users] AMINOACIDS
Dear Justin I usepropka site for pKa calculation but I want to know if pKa is smaller than my desired pH , I must consider this amino acid deprotonate? and if pKa of aminoacids is bigger thanmy desired pH, I must protonate this amino acid? Thank you Fatemeh Ramezani - Forwarded Message - From: Justin Lemkul jalem...@vt.edu To: fatemeh ramezani fr_...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, 15 July 2013, 17:00 Subject: Re: [gmx-users] AMINOACIDS On 7/15/13 7:56 AM, fatemeh ramezani wrote: Dear Justin I don't know how can I detect the protonation state of amino acids in specific pH. Can you help me? There are various methods for pKa calculations, and based on those results you can choose the appropriate states with pdb2gmx command-line options. Again, this topic is covered extensively in the archive and you would benefit from some of the previous discussions that I will not repeat here. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Associate 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 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Using the checkpoint file to restore corrupt trajectory.
I guess, the more important question is whether the checkpoint file stores the previous checkpoints as well. If it stores only the last checkpoint at 20 ns, then I guess there is no way to rerun from 18 ns. I do not store a .trr because of space constraints and hence I do not have the velocities. otherwise, I would have used the snapshot from 18ns and extended the simulation. Now, it looks like I will have to re-generate the velocities and re-equilibrate the system. On Mon, Jul 15, 2013 at 6:22 PM, rajat desikan rajatdesi...@gmail.comwrote: Hi Justin, The checkpoint file has gone on to 20 ns. If I do a rerun, the simulation will finish in one step. On Mon, Jul 15, 2013 at 6:11 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/15/13 8:38 AM, Rajat Desikan wrote: Hi, I have a 20 ns long trajectory which has become corrupted beyond 18ns. I have the full checkpoint file. Is there any way I can use mdrun and the .cpt to rerun the simulation from 18ns and append it to the current .xtc (After I have clipped the part beyond 18ns by trjconv)? I did not find the appropriate flag in the mdrun online manual pages. It's no different than doing any restart. mdrun -s topol.tpr -cpi good_state.cpt -noappend Then concatenate trajectory and energy files with trjcat and eneconv. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Associate Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu| (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Using the checkpoint file to restore corrupt trajectory.
On 7/15/13 8:52 AM, rajat desikan wrote: Hi Justin, The checkpoint file has gone on to 20 ns. If I do a rerun, the simulation will finish in one step. You need a checkpoint file that corresponds to a good frame before the corruption. If you don't have that, you can't fix the broken trajectory. Your first message implied that you had a good frame. Since that's not the case, you'll have to either re-run the simulation or skip the bad frame and settle for fewer data points. -Justin On Mon, Jul 15, 2013 at 6:11 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/15/13 8:38 AM, Rajat Desikan wrote: Hi, I have a 20 ns long trajectory which has become corrupted beyond 18ns. I have the full checkpoint file. Is there any way I can use mdrun and the .cpt to rerun the simulation from 18ns and append it to the current .xtc (After I have clipped the part beyond 18ns by trjconv)? I did not find the appropriate flag in the mdrun online manual pages. It's no different than doing any restart. mdrun -s topol.tpr -cpi good_state.cpt -noappend Then concatenate trajectory and energy files with trjcat and eneconv. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Associate Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- == Justin A. Lemkul, Ph.D. Postdoctoral Associate 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 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: Fw: [gmx-users] AMINOACIDS
On 7/15/13 8:54 AM, fatemeh ramezani wrote: Dear Justin I usepropka site for pKa calculation but I want to know if pKa is smaller than my desired pH , I must consider this amino acid deprotonate? and if pKa of aminoacids is bigger thanmy desired pH, I must protonate this amino acid? Please consult any basic biochemistry text and/or website describing the Henderson-Hasselbalch equation. -Justin Thank you Fatemeh Ramezani - Forwarded Message - From: Justin Lemkul jalem...@vt.edu To: fatemeh ramezani fr_...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, 15 July 2013, 17:00 Subject: Re: [gmx-users] AMINOACIDS On 7/15/13 7:56 AM, fatemeh ramezani wrote: Dear Justin I don't know how can I detect the protonation state of amino acids in specific pH. Can you help me? There are various methods for pKa calculations, and based on those results you can choose the appropriate states with pdb2gmx command-line options. Again, this topic is covered extensively in the archive and you would benefit from some of the previous discussions that I will not repeat here. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Associate 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 == -- == Justin A. Lemkul, Ph.D. Postdoctoral Associate 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 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Using the checkpoint file to restore corrupt trajectory.
On 7/15/13 8:56 AM, rajat desikan wrote: I guess, the more important question is whether the checkpoint file stores the previous checkpoints as well. If it stores only the last checkpoint at 20 ns, then I guess there is no way to rerun from 18 ns. It does not. Checkpoints are recycled every -cpt minutes. You can keep all checkpoints by using the mdrun -cpnum option, but I suspect that will use up a lot of disk space. I do not store a .trr because of space constraints and hence I do not have the velocities. otherwise, I would have used the snapshot from 18ns and extended the simulation. Now, it looks like I will have to re-generate the velocities and re-equilibrate the system. Or just re-run the simulation from the same .tpr file you used before. -Justin On Mon, Jul 15, 2013 at 6:22 PM, rajat desikan rajatdesi...@gmail.comwrote: Hi Justin, The checkpoint file has gone on to 20 ns. If I do a rerun, the simulation will finish in one step. On Mon, Jul 15, 2013 at 6:11 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/15/13 8:38 AM, Rajat Desikan wrote: Hi, I have a 20 ns long trajectory which has become corrupted beyond 18ns. I have the full checkpoint file. Is there any way I can use mdrun and the .cpt to rerun the simulation from 18ns and append it to the current .xtc (After I have clipped the part beyond 18ns by trjconv)? I did not find the appropriate flag in the mdrun online manual pages. It's no different than doing any restart. mdrun -s topol.tpr -cpi good_state.cpt -noappend Then concatenate trajectory and energy files with trjcat and eneconv. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Associate Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu| (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- == Justin A. Lemkul, Ph.D. Postdoctoral Associate 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 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Using the checkpoint file to restore corrupt trajectory.
Thank you! On Mon, Jul 15, 2013 at 6:29 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/15/13 8:56 AM, rajat desikan wrote: I guess, the more important question is whether the checkpoint file stores the previous checkpoints as well. If it stores only the last checkpoint at 20 ns, then I guess there is no way to rerun from 18 ns. It does not. Checkpoints are recycled every -cpt minutes. You can keep all checkpoints by using the mdrun -cpnum option, but I suspect that will use up a lot of disk space. I do not store a .trr because of space constraints and hence I do not have the velocities. otherwise, I would have used the snapshot from 18ns and extended the simulation. Now, it looks like I will have to re-generate the velocities and re-equilibrate the system. Or just re-run the simulation from the same .tpr file you used before. -Justin On Mon, Jul 15, 2013 at 6:22 PM, rajat desikan rajatdesi...@gmail.com wrote: Hi Justin, The checkpoint file has gone on to 20 ns. If I do a rerun, the simulation will finish in one step. On Mon, Jul 15, 2013 at 6:11 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/15/13 8:38 AM, Rajat Desikan wrote: Hi, I have a 20 ns long trajectory which has become corrupted beyond 18ns. I have the full checkpoint file. Is there any way I can use mdrun and the .cpt to rerun the simulation from 18ns and append it to the current .xtc (After I have clipped the part beyond 18ns by trjconv)? I did not find the appropriate flag in the mdrun online manual pages. It's no different than doing any restart. mdrun -s topol.tpr -cpi good_state.cpt -noappend Then concatenate trajectory and energy files with trjcat and eneconv. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Associate Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.edu jalemkul@outerbanks.** umaryland.edu jalem...@outerbanks.umaryland.edu| (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Associate Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] snapshot
Hi, The following command I used for the snapshots but I'm getting one frame time 0 time 500. what are the changes I need to do in the command to get snapshots in equal intervals of time for ex: 250ps. My production MD trajectory was 15ns. g_trjconv -s md.tpr -f md.trr -o beta.gro -skip 1 -dt 0 -dump 0 -sep Thanks in Advance. Rama On Mon, Jul 15, 2013 at 2:02 AM, Dr. Vitaly Chaban vvcha...@gmail.comwrote: look for either -dt or -skip. Dr. Vitaly V. Chaban On Mon, Jul 15, 2013 at 2:03 AM, Rama ramkishn...@gmail.com wrote: Hi, How to get a snapshots in equal intervals of time (250ps) from production MD trajectory. I'm using -sep , -t0, -timestep but output came only one .gro file. -- View this message in context: http://gromacs.5086.x6.nabble.com/snapshot-tp5009837.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] snapshot
On 7/15/13 9:02 AM, Rama Krishna Koppisetti wrote: Hi, The following command I used for the snapshots but I'm getting one frame time 0 time 500. what are the changes I need to do in the command to get snapshots in equal intervals of time for ex: 250ps. My production MD trajectory was 15ns. g_trjconv -s md.tpr -f md.trr -o beta.gro -skip 1 -dt 0 -dump 0 -sep The interval depends on how often you saved snapshots. You do not need -dt and -dump options. You will get separate coordinate files with -sep and the correct value of -skip will give you what you want. If you saved a frame every 50 ps, then trjconv -skip 5 -sep will give you a frame every 250 ps. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Associate 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 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] snapshot
Thank you very much *Justin*. -- Rama On Mon, Jul 15, 2013 at 8:06 AM, Justin Lemkul jalem...@vt.edu wrote: On 7/15/13 9:02 AM, Rama Krishna Koppisetti wrote: Hi, The following command I used for the snapshots but I'm getting one frame time 0 time 500. what are the changes I need to do in the command to get snapshots in equal intervals of time for ex: 250ps. My production MD trajectory was 15ns. g_trjconv -s md.tpr -f md.trr -o beta.gro -skip 1 -dt 0 -dump 0 -sep The interval depends on how often you saved snapshots. You do not need -dt and -dump options. You will get separate coordinate files with -sep and the correct value of -skip will give you what you want. If you saved a frame every 50 ps, then trjconv -skip 5 -sep will give you a frame every 250 ps. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Associate Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: Fw: [gmx-users] AMINOACIDS
On 7/15/13 9:11 AM, fatemeh ramezani wrote: Dear Justin I know the Henderson-Hasselbalch equation, but what should I consider [A-]/[HA] for amino acids? That's what you're solving for. You know pH and pKa, and that tells you the ratio of deprotonated to protonated species, which tells you which one predominates and therefore how you should treat them in the topology. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Associate 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 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: snapshot
Hi, the following: trjconv -s md.tpr -f md.trr -o beta.gro -dt 250 -sep should work. -dt 250 ; write output every 250 ps -sep ; to write each frame (but the output frequency gets overwritten by '-dt 250') the additional use of '-dump x' might be the problem, since with '-dump x' GMX writes only the frame at time x Greetings Thomas Am 15.07.2013 15:03, schrieb gmx-users-requ...@gromacs.org: Hi, The following command I used for the snapshots but I'm getting one frame time 0 time 500. what are the changes I need to do in the command to get snapshots in equal intervals of time for ex: 250ps. My production MD trajectory was 15ns. g_trjconv -s md.tpr -f md.trr -o beta.gro -skip 1 -dt 0 -dump 0 -sep Thanks in Advance. Rama On Mon, Jul 15, 2013 at 2:02 AM, Dr. Vitaly Chaban vvcha...@gmail.comwrote: look for either -dt or -skip. Dr. Vitaly V. Chaban On Mon, Jul 15, 2013 at 2:03 AM, Ramaramkishn...@gmail.com wrote: Hi, How to get a snapshots in equal intervals of time (250ps) from production MD trajectory. I'm using -sep , -t0, -timestep but output came only one .gro file. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: snapshot
Thanks *Thomas* --Rama On Mon, Jul 15, 2013 at 9:00 AM, Thomas Schlesier schl...@uni-mainz.dewrote: Hi, the following: trjconv -s md.tpr -f md.trr -o beta.gro -dt 250 -sep should work. -dt 250 ; write output every 250 ps -sep ; to write each frame (but the output frequency gets overwritten by '-dt 250') the additional use of '-dump x' might be the problem, since with '-dump x' GMX writes only the frame at time x Greetings Thomas Am 15.07.2013 15:03, schrieb gmx-users-requ...@gromacs.org: Hi, The following command I used for the snapshots but I'm getting one frame time 0 time 500. what are the changes I need to do in the command to get snapshots in equal intervals of time for ex: 250ps. My production MD trajectory was 15ns. g_trjconv -s md.tpr -f md.trr -o beta.gro -skip 1 -dt 0 -dump 0 -sep Thanks in Advance. Rama On Mon, Jul 15, 2013 at 2:02 AM, Dr. Vitaly Chaban vvcha...@gmail.comwrote: look for either -dt or -skip. Dr. Vitaly V. Chaban On Mon, Jul 15, 2013 at 2:03 AM, Ramaramkishn...@gmail.com wrote: Hi, How to get a snapshots in equal intervals of time (250ps) from production MD trajectory. I'm using -sep , -t0, -timestep but output came only one .gro file. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] RE: Is non-linear data output/storage possible?
Justin Lemkul wrote The .cpt file stores information related to output frequency. The existing.cpt file designates output every X steps, while the new .tpr file specifies output every Y steps, and X != Y, so mdrun complains. I'm assuming mdrun aborts at that point? Have you tried with -noappend? The information on the extending simulations page does not seem to agree with what you just said above. It says : If you wish/need to change .mdp file options, then either grompp -f new.mdp -c old.tpr -o new.tpr -t old.cpt mdrun -s new.tpr or grompp -f new.mdp -c old.tpr -o new.tpr mdrun -s new.tpr -cpi old.cpt should work. I am simply changing the mdp file options so the difference in output frequency shouldn't actually cause mdrun to abort. Justin Lemkul wrote The analysis tools will complain, anyway. Whenever a program encounters a non-uniform frame interval, it aborts, IIRC. I am not planning on using most of the Gromacs analysis tools either way, so hopefully this won't be too much of a problem. -- View this message in context: http://gromacs.5086.x6.nabble.com/Is-non-linear-data-output-storage-possible-tp5008858p5009866.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] RE: Is non-linear data output/storage possible?
On 7/15/13 11:48 AM, Neha wrote: Justin Lemkul wrote The .cpt file stores information related to output frequency. The existing.cpt file designates output every X steps, while the new .tpr file specifies output every Y steps, and X != Y, so mdrun complains. I'm assuming mdrun aborts at that point? Have you tried with -noappend? The information on the extending simulations page does not seem to agree with what you just said above. It says : If you wish/need to change .mdp file options, then either grompp -f new.mdp -c old.tpr -o new.tpr -t old.cpt mdrun -s new.tpr or grompp -f new.mdp -c old.tpr -o new.tpr mdrun -s new.tpr -cpi old.cpt should work. I am simply changing the mdp file options so the difference in output frequency shouldn't actually cause mdrun to abort. That section of the wiki was written years ago, when the default behavior of mdrun was to not append files unless specifically requested. Now that mdrun does append by default (as of version 4.5), you probably have to add -noappend. If that works, then I'm happy to update the wiki, but since what you're trying to do is not common, there was no compelling need to update the wiki to reflect the difference. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Associate 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 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] How to make changes on Trajectory file?
Hi, I saved my coordinates every 500ps in production MD run, could I alter now .xtc file by saving different coordinates for ex: every 100ps. Is there any command to alter the files. Thanks in Advance --Rama -- View this message in context: http://gromacs.5086.x6.nabble.com/How-to-make-changes-on-Trajectory-file-tp5009868.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] How to make changes on Trajectory file?
On 7/15/13 12:08 PM, Rama wrote: Hi, I saved my coordinates every 500ps in production MD run, could I alter now .xtc file by saving different coordinates for ex: every 100ps. Is there any command to alter the files. You can't create frames that aren't there. You can decrease the frame interval using trjconv -skip, but you can't perform magic the other way around. -Justin -- == Justin A. Lemkul, Ph.D. 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 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] How to make changes on Trajectory file?
O kay... T hanks for prompt reply *Justin* * . --Rama ** * On Mon, Jul 15, 2013 at 11:11 AM, Justin Lemkul jalem...@vt.edu wrote: On 7/15/13 12:08 PM, Rama wrote: Hi, I saved my coordinates every 500ps in production MD run, could I alter now .xtc file by saving different coordinates for ex: every 100ps. Is there any command to alter the files. You can't create frames that aren't there. You can decrease the frame interval using trjconv -skip, but you can't perform magic the other way around. -Justin -- ==** Justin A. Lemkul, Ph.D. 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 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Aw: Re: [gmx-users] How to calculate enthalpy
Whats the energy of each waters hydrogen bonding strength respective of each one...as they vary by a couple kcal/mol according to the new IUPAC standard deffinition of hydrogen bonds (2011)? And the energy of the internal structural hydrogen bonds that were disrupted? Assuming no acidic enviornment where electrons are involved...means of coarse... Gesendet:Montag, 15. Juli 2013 um 10:34 Uhr Von:pooja_gu...@nccs.res.in An:vvcha...@gmail.com, Discussion list for GROMACS users gmx-users@gromacs.org Betreff:Re: [gmx-users] How to calculate enthalpy Thanks Vitaly but how?? lets say the difference between unfolded to folded protein is 100 water molecules. What is the correct procedure to calculate (theoretically) the entrapy correspond to single water molecule for stabilizing/destabilizing the protein. help me Sure, you can. Dr. Vitaly V. Chaban On Mon, Jul 15, 2013 at 8:38 AM, pooja_gu...@nccs.res.in wrote: Hi I want calculate the enthalpy of water molecule corresponding to protein folded and unfolded state. How much a single water molecule (enthalpy and free energy) contribute in folding ? Can we calculate enthapy from g_energy? -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please dont post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Cant post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please dont post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Cant post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please dont post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Cant post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: enery conserving problem in NVE simulations with SMW4-NPD polarizable force field
On Mon, Jul 15, 2013 at 3:00 AM, gmx-users-requ...@gromacs.org wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. Re: How to calculate enthalpy (Dr. Vitaly Chaban) 2. enery conserving problem in NVE simulations with SMW4-NPD polarizable force field (Ding Yun) -- Message: 2 Date: Mon, 15 Jul 2013 09:43:38 + From: Ding Yun yun.d...@phys.chem.ethz.ch Subject: [gmx-users] enery conserving problem in NVE simulations with SMW4-NPD polarizable force field To: gmx-users@gromacs.org gmx-users@gromacs.org Message-ID: e82f84d319900f4ca5fcf4b9bb98716c16242...@mbx23.d.ethz.ch Content-Type: text/plain; charset=iso-8859-1 Hello, I'm trying to simulate liquid water (512 water molecules) with SMW4-NPD polarizable force field. The NVT simulation looks fine, but when I restart it with NVE runs, the total energy of the system keeps drifting down. The time step I'm using now is 0.5 fs and emtol=0.01 kJ/mol/nm. Gromacs is also compiled with double precision. Does anyone have any suggestions for this kind of problem? Thanks a lot. Regards, Yun My .mdp file: ; RUN CONTROL PARAMETERS integrator = md tinit= 800 init_step=0 dt = 0.0005 ; time step (ps) nsteps = 40 ; number of steps ; OUTPUT CONTROL OPTIONS nstenergy= 100 nstxout =100 ; NEIGHBORSEARCHING PARAMETERS nstlist = -1 ns_type = grid pbc = xyz rlist= 1.24 ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype = PME-Switch rcoulomb = 1.05 rcoulomb_switch = 0.85 vdw-type = shift rvdw = 1.05 ewald_rtol =1e-4 ; OPTIONS FOR BONDS constraints = h-bonds ; Type of constraint algorithm constraint-algorithm = Lincs ; Polarizable model parameters emtol = 0.01 niter = 20 ; Temperature coupling tcoupl = no ; pressure coupling pcoupl= no ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = no -- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! End of gmx-users Digest, Vol 111, Issue 69 ** Try the following for options for bonds. constraint-algorithm = shake shake-tol= 1e-10 I hope this helps. -- *S. Alireza Bagherzadeh, M.A.Sc. https://circle.ubc.ca/handle/2429/26269 * * * *PhD Candidate * * * *Dept. of Chem. Bio. Eng. http://www.chbe.ubc.ca/* * * *University of BC http://www.ubc.ca/ * *T: *604.827.3194* | C: *778.990.1383* | F: *604.822.6003* * ** * * *6.03 - 2360 East Mall* * * *Vancouver BC V6T1Z3* ***Success is not final, failure is not fatal: it is the courage to continue that counts. --W. S. Churchill* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Reverse_MICELLEFatel error, moleculetype SOL is redefined
Hi Gromaxers, Thanks for previous answers. I have to simulate reverse micelle after solvation with isooctane.My system now is: ISOOCTANE(solvent)+AOT(surfactant)+coreWATER. When I do grompp, it says moleculetype SOL is redefined and lots of another errors. Please advice me how do I do reverse micelle simulation. What I did is:: (1) pdb2gmx -f RM.pdb -o RM.gro -p RM.top step I choose isooctane as water model. I have isooctane.itp in the file watermodel.dat inside my forcefield. (2) editconf -c -f RM.gro -o RM1.gro -p RM.top -bt dodecahedron -d 2.0 -shell 0.3 (3) genbox -cp RM.gro -cs isooctane.gro -p reverse_RM.top -o RM2.pdb (4) grompp -f em.mdp -c RM2.pdb -p RM.top -n index.ndx -o em.tpr -maxwarn 5 where RM.pdb is pdb file of reverse micelle All required files I have ,and I have index.ndx file also But it returns : Fatel error: the moleculetype SOL is redefined I tried lots, I change the SOL to WATER every where in frocefield as well as my .gro file too. I tried all what I could but no get any benifit. So Please advice me how do I do this. Thanks for your help. Hari -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Chlorate ion force field
Dear users, How do I get the force-field for ClO4- ion in the gromacs? Thanks in advance. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
