Re: [gmx-users] Salt Bridge
Hi, I want to know the default cutoff distance g_saltbr tool uses in identifying the salt-bridges.. Regards -- Bharat -- 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] Hbonds per residue
Dear gromacs users, I have used g_hbond with -hbn option to generate a .ndx file. There is a method to plot the number of hbonds per residue in gromacs 4.5.5??? This issue is very confuse. Thanks for any suggestion!!! -- Natalia Alveal Fuentealba Ingeniera en Bioinformática Laboratory of Membranes Proteins Structure and Signalling Departamento de Fisiología Pontificia Universidad Católica de Chile Alameda 340, Santiago, Chile Fono: 56-2-3542877 -- 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] Interaction energy between helices
On 6/11/14, 5:36 PM, Natalia Alveal F. wrote: Dear Gromacs users, I want to calculate the energy of interaction between two helices of a protein, but g_energy dont have the option for -ndx file to select these specific residues of a helix. How I can do this? That's what energygrps in the .mdp file are for. Re-calculate the energies with mdrun -rerun using the new .tpr file. -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] how many groups shall I use to control the temperature?
Dear justin, I have doubts that whether I should use two groups to control the temperature or just one since there are just 604 hundred Protein beads and 6+ solvent beads. It is said that two groups are more accurate but when when i split them into two groups Protein nonProtein, I found that fluctulation of temperature in group Protein are obvious, Im afraid that would have an effect on accuracy on my simulation results. So how many groups shall I use to control the temperature? Thanks in advance regards, chen -- 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] Why does the list keep unsubscribing me?
This is the 4th time I am thrown out of the list by some random phishing email and I am done with this. If I am thrown out this time (I know I will be and no-one cares to fix any issues), I am not coming back. I just came back the last time to thank you folks for all your comments and helps regarding gromacs.have fun !! From: xru...@live.com To: gmx-us...@gromacs.org Date: Mon, 2 Jun 2014 04:16:24 + Subject: 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. -- 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] Why does the list keep unsubscribing me?
Hi, One simple solution is to subscribe with a different email address. Mark On Thu, Jun 12, 2014 at 9:54 AM, X Rules xru...@live.com wrote: This is the 4th time I am thrown out of the list by some random phishing email and I am done with this. If I am thrown out this time (I know I will be and no-one cares to fix any issues), I am not coming back. I just came back the last time to thank you folks for all your comments and helps regarding gromacs.have fun !! From: xru...@live.com To: gmx-us...@gromacs.org Date: Mon, 2 Jun 2014 04:16:24 + Subject: 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. -- 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.
Re: [gmx-users] Hbonds per residue
Hi Natalia, It's a feature that has been requested a number of times, but has not been implemented yet unfortunately. Erik On 12 Jun 2014, at 00:50, Natalia Alveal F. nalv...@bio.puc.cl wrote: Dear gromacs users, I have used g_hbond with -hbn option to generate a .ndx file. There is a method to plot the number of hbonds per residue in gromacs 4.5.5??? This issue is very confuse. Thanks for any suggestion!!! -- Natalia Alveal Fuentealba Ingeniera en Bioinformática Laboratory of Membranes Proteins Structure and Signalling Departamento de Fisiología Pontificia Universidad Católica de Chile Alameda 340, Santiago, Chile Fono: 56-2-3542877 -- 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] Energy minimisation step in Lipid protein simulation
Dear friends, In protein lipid simulation , when I do energy minimisation ster I get an error as Ek! No confout.gro at all! Died at inflategro.pl line 104. What is confout.gro. If am right it is the output file that we get from the minimisation step. I used the command perl inflategro.pl confout.gro 0.95 POPC 0 system_shrink1.gro 5 area_shrink1.dat. Please help me. regards, Suriyanarayanan. -- 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] energy minimisation step in lipid protein simulation
Dear friends, In protein lipid simulation , when I do energy minimisation ster I get an error as Ek! No confout.gro at all! Died at inflategro.pl line 104. What is confout.gro. If am right it is the output file that we get from the minimisation step. I used the command perl inflategro.pl confout.gro 0.95 POPC 0 system_shrink1.gro 5 area_shrink1.dat. Please help me. regards, Suriyanarayanan. -- 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] energy minimisation step in protein lipid simulation
Dear friends, In protein lipid simulation , when I do energy minimisation ster I get an error as Ek! No confout.gro at all! Died at inflategro.pl line 104. What is confout.gro. If am right it is the output file that we get from the minimisation step. I used the command perl inflategro.pl confout.gro 0.95 POPC 0 system_shrink1.gro 5 area_shrink1.dat. Please help me. regards, Suriyanarayanan. -- 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] pH simulation
Hi everyone... I want to do pH simulation in gromacs . I didn't found any specific link that I can follow for calculation regarding pH . Can you please guide me ..Any link that can help me... Thanks in advance Regards Lovika -- 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] pH simulation
Hi, http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation Gromacs users list: http://comments.gmane.org/gmane.science.biology.gromacs.user/40950 https://www.mail-archive.com/gmx-users@gromacs.org/msg05430.html On Thu, Jun 12, 2014 at 2:44 PM, Lovika Moudgil lovikamoud...@gmail.com wrote: Hi everyone... I want to do pH simulation in gromacs . I didn't found any specific link that I can follow for calculation regarding pH . Can you please guide me ..Any link that can help me... Thanks in advance Regards Lovika -- 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. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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] energy minimisation in lipid protein simulation
Dear friends, In protein lipid simulation , when I do energy minimisation ster I get an error as Ek! No confout.gro at all! Died at inflategro.pl line 104. What is confout.gro. If am right it is the output file that we get from the minimisation step. I used the command perl inflategro.pl confout.gro 0.95 POPC 0 system_shrink1.gro 5 area_shrink1.dat. Please help me. regards, Suriyanarayanan. -- 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] (no subject)
Dear friends, In protein lipid simulation , when I do energy minimisation ster I get an error as Ek! No confout.gro at all! Died at inflategro.pl line 104. What is confout.gro. If am right it is the output file that we get from the minimisation step. I used the command perl inflategro.pl confout.gro 0.95 POPC 0 system_shrink1.gro 5 area_shrink1.dat. Please help me. regards, Suriyanarayanan. -- 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] (no subject)
On 6/12/14, 5:31 AM, Balasubramanian Suriyanarayanan wrote: Why is my questions not appearing in the forum. Do I not follow the rules.' Please clarify. Your messages are being posted just fine. Please stop spamming the list. -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] Energy minimisation step in Lipid protein simulation
On 6/12/14, 4:54 AM, Balasubramanian Suriyanarayanan wrote: Dear friends, In protein lipid simulation , when I do energy minimisation ster I get an error as Ek! No confout.gro at all! Died at inflategro.pl line 104. What is confout.gro. If am right it is the output file that we get from the minimisation step. I used the command perl inflategro.pl confout.gro 0.95 POPC 0 system_shrink1.gro 5 area_shrink1.dat. You're specifying confout.gro as the source of coordinates. Apparently that file doesn't exist in the working directory, so InflateGRO is giving you an error. -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] how many groups shall I use to control the temperature?
On 6/12/14, 2:37 AM, 陈功 wrote: Dear justin, I have doubts that whether I should use two groups to control the temperature or just one since there are just 604 hundred Protein beads and 6+ solvent beads. It is said that two groups are more accurate but when when i split them into two groups Protein nonProtein, I found that fluctulation of temperature in group Protein are obvious, Im afraid that would have an effect on accuracy on my simulation results. So how many groups shall I use to control the temperature? What protocol is used in published studies similar to what you're doing? Small groups will have larger fluctuations in temperature, that's a given. I don't do CG simulations, so I don't know how such groups are commonly treated. -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] -inf potential with TPIC
On 6/11/14, 8:55 PM, Rafael I. Silverman y de la Vega wrote: I mistyped amber, when I should have typed charmm, amber is totally uninvolved in my calculations. I used the script from http://www.gromacs.org/Downloads/User_contributions/Other_software titled charmm2gromacs. The output looked fine after running it. And, I doubt its the cofactor, just ran the insertion with double precision mdrun, it gave reasonable looking results. There seems to be some sort of issue with unreasonable interaction energies not being discarded properly. It's entirely possible that there's something wrong with the tpic code; you can certainly file a bug report on Redmine with input files to reproduce it. -Justin On Tue, Jun 10, 2014 at 3:41 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/10/14, 6:14 PM, Rafael I. Silverman y de la Vega wrote: I meant that I only changed to cofactor to gromacs chamm27 format, not amber format. I used charmm27 for the apoprotein as well as the cofactor. What script did you use? I don't understand why Amber99SB is involved here, so I don't know exactly what you were doing to create the topology. It may not end up being useful information, but it's important to establish the validity of the underlying physical model. -Justin On Tue, Jun 10, 2014 at 3:09 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/10/14, 6:04 PM, Rafael I. Silverman y de la Vega wrote: you think it was the cofactor model? If you're using a CHARMM-parametrized cofactor with an Amber99SB protein, I'd say the simulations are wholly unreliable. It's certainly the #1 likely cause for nonsensical results. If you want to get to the root of the issue, you need to start with a solid foundation. Unless that's not what your last message meant? When you say only changed the cofactor, that implied to me that you didn't consistently convert everything in the system. -Justin On Tue, Jun 10, 2014 at 2:23 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/10/14, 5:01 PM, Rafael I. Silverman y de la Vega wrote: wait, I only changed the cofactor to gromacs charmm27.ff format Pretty amazing that the simulation even ran with that mash-up of parameters :) I'd say that's the most likely cause of your problems; nonsensical physical model leads to nonsensical output. -Justin On Tue, Jun 10, 2014 at 1:58 PM, Rafael I. Silverman y de la Vega rsilv...@ucsc.edu wrote: I suppose something might be wrong with the simulations. I am using gromacs 4.6.5, I am simulating a protein with a cofactor, someone else parametrized it, I changed from charmm to gromacs amber99sb.ff format with a script on the gromacs website. I did a typical em/nvt/npt equilibration followed by a 5 ns production run. I picked 250 frames out of the trajectory, and altered them to the TPIC input format with a script I wrote, to insert the particle half way between two atoms that I chose. I am inserting a water molecule. When I run the actual insertion some of the frames have a reasonable looking mu, and some have -inf mu. I think it may have to do with cavity size, some frames have too small of a cavity, so the interaction energy of the inserted water diverges... On Mon, Jun 9, 2014 at 6:40 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/9/14, 6:41 PM, Rafael I. Silverman y de la Vega wrote: Hi all, I am having a problem with -inf mu coming out of TPIC calculations. Anyone have some suggestions on how to avoid this? Tabulated potentials? Or can I modify the source code to reject the absurd values that cause this? I read a few old discussions on this, I didnt see much on how to handle this. I'd be much more concerned that something is going wrong in the simulations. I have no experience with TPIC, but if you post more detailed information about what you're doing and which Gromacs version you're using, you're more likely to get some suggestions. -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. -- == 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,
Re: [gmx-users] (no subject)
i've recieved your email concernig energy minimisation step in protein lipid simulation already 3 times .. maybe you've deactivated the delivery of mails? if so, do the following: go to https://mailman-1.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users and log in where it says To unsubscribe from gromacs.org_gmx-users, get a password reminder, or change your subscription options enter your subscription email address: there you can change your personal settings. vedat Am 12.06.2014 11:31, schrieb Balasubramanian Suriyanarayanan: Why is my questions not appearing in the forum. Do I not follow the rules.' Please clarify. regards Suriyanarayanan -- 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] (no subject)
then, i don't know what to do. may be your email provider sorts them out or something. anyway, did you get justin's answer he sent recently? see below .. vedat On 6/12/14, 4:54 AM, Balasubramanian Suriyanarayanan wrote: Dear friends, In protein lipid simulation , when I do energy minimisation ster I get an error as Ek! No confout.gro at all! Died at inflategro.pl line 104. What is confout.gro. If am right it is the output file that we get from the minimisation step. I used the command perl inflategro.pl confout.gro 0.95 POPC 0 system_shrink1.gro 5 area_shrink1.dat. You're specifying confout.gro as the source of coordinates. Apparently that file doesn't exist in the working directory, so InflateGRO is giving you an error. -Justin Am 12.06.2014 11:46, schrieb Balasubramanian Suriyanarayanan: but I get other mails. even the last one which i have sent with out title has appeared. regards Suriyanarayanan On Thu, Jun 12, 2014 at 3:14 PM, Vedat Durmaz dur...@zib.de mailto:dur...@zib.de wrote: i've recieved your email concernig energy minimisation step in protein lipid simulation already 3 times .. maybe you've deactivated the delivery of mails? if so, do the following: go to https://mailman-1.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users and log in where it says To unsubscribe from gromacs.org_gmx-users, get a password reminder, or change your subscription options enter your subscription email address: there you can change your personal settings. vedat Am 12.06.2014 11:31, schrieb Balasubramanian Suriyanarayanan: Why is my questions not appearing in the forum. Do I not follow the rules.' Please clarify. regards Suriyanarayanan -- 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] (no subject)
i've recieved your email concernig energy minimisation step in protein lipid simulation already 3 times .. maybe you've deactivated the delivery of mails? if so, do the following: go to https://mailman-1.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users and log in where it says To unsubscribe from gromacs.org_gmx-users, get a password reminder, or change your subscription options enter your subscription email address: there you can change your personal settings. vedat Am 12.06.2014 11:31, schrieb Balasubramanian Suriyanarayanan: Why is my questions not appearing in the forum. Do I not follow the rules.' Please clarify. regards Suriyanarayanan -- 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] Tc grps, one group or two?
On Thu, Jun 12, 2014 at 4:11 AM, 陈功 gchen...@gmail.com wrote: Dear gromacs users, I have doubts that whether I should use two groups to control the temperature or just one since there are just 604 hundred Protein beads and 6+ solvent beads. It is said that two groups are more accurate but when when i split them into two groups Protein nonProtein, I found that fluctulation of temperature in group Protein are obvious, Im afraid that would have an effect on accuracy on my simulation results. Can anyone help me ? thanks in advance This is a complex issue. Even with a proper thermostat (i.e not Berendsen), making a sound observation of temperature is tricky. See http://www.deshawresearch.com/publications/Equipartition%20and%20the%20Calculation%20of%20Temperature%20in%20Biomolecular%20Simulations.pdf Measuring and managing temperature in the presence of other possible problems (invalid or non-transferable force-field parameters, non-conservative integration schemes) is even harder. Whether any of this is relevant to your intended observables is usually unknown, because typically no previous work was based on simulations sufficiently converged to be definitive. With orders of magnitude more solvent than solute, I would generally suggest a single temperature-coupling group, but there may be issues with how your coarse-grained force field was parameterized of which I am unaware. Mark regards, chen -- 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.
Re: [gmx-users] Energy minimisation step in Lipid protein simulation
But is not confout.gro the output of the compression step. the command is perl inflategro.pl system.gro 4 POPC 0 system_inflated.gro 5 area.dat or else what is the output of above command. regards suriyanarayanan On Thu, Jun 12, 2014 at 3:13 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/12/14, 4:54 AM, Balasubramanian Suriyanarayanan wrote: Dear friends, In protein lipid simulation , when I do energy minimisation ster I get an error as Ek! No confout.gro at all! Died at inflategro.pl line 104. What is confout.gro. If am right it is the output file that we get from the minimisation step. I used the command perl inflategro.pl confout.gro 0.95 POPC 0 system_shrink1.gro 5 area_shrink1.dat. You're specifying confout.gro as the source of coordinates. Apparently that file doesn't exist in the working directory, so InflateGRO is giving you an error. -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. -- 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] Why does the list keep unsubscribing me?
Thanks for the solution Mark, but from what I feel the right way to do is to fix mailman (add another option of clicking a link sent to your email to confirm unsubscribe, the same way subscription works). I might not be the only one, or may be I am the only one complaining :). Lets see how long this lasts,Abhi Date: Thu, 12 Jun 2014 10:22:48 +0200 From: mark.j.abra...@gmail.com To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Why does the list keep unsubscribing me? Hi, One simple solution is to subscribe with a different email address. Mark On Thu, Jun 12, 2014 at 9:54 AM, X Rules xru...@live.com wrote: This is the 4th time I am thrown out of the list by some random phishing email and I am done with this. If I am thrown out this time (I know I will be and no-one cares to fix any issues), I am not coming back. I just came back the last time to thank you folks for all your comments and helps regarding gromacs.have fun !! From: xru...@live.com To: gmx-us...@gromacs.org Date: Mon, 2 Jun 2014 04:16:24 + Subject: 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. -- 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.
Re: [gmx-users] Energy minimisation step in Lipid protein simulation
On 6/12/14, 7:14 AM, Balasubramanian Suriyanarayanan wrote: But is not confout.gro the output of the compression step. the command is perl inflategro.pl system.gro 4 POPC 0 system_inflated.gro 5 area.dat or else what is the output of above command. Read the InflateGRO documentation (top of the script). -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] Why does the list keep unsubscribing me?
Hi, I've no idea if mailman even has that option, or the KTH IT admins would be willing to set it up, but that's not worth exploring until automatic unsubscription is known to be a problem for more than one email address. Mark On Thu, Jun 12, 2014 at 1:34 PM, X Rules xru...@live.com wrote: Thanks for the solution Mark, but from what I feel the right way to do is to fix mailman (add another option of clicking a link sent to your email to confirm unsubscribe, the same way subscription works). I might not be the only one, or may be I am the only one complaining :). Lets see how long this lasts,Abhi Date: Thu, 12 Jun 2014 10:22:48 +0200 From: mark.j.abra...@gmail.com To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Why does the list keep unsubscribing me? Hi, One simple solution is to subscribe with a different email address. Mark On Thu, Jun 12, 2014 at 9:54 AM, X Rules xru...@live.com wrote: This is the 4th time I am thrown out of the list by some random phishing email and I am done with this. If I am thrown out this time (I know I will be and no-one cares to fix any issues), I am not coming back. I just came back the last time to thank you folks for all your comments and helps regarding gromacs.have fun !! From: xru...@live.com To: gmx-us...@gromacs.org Date: Mon, 2 Jun 2014 04:16:24 + Subject: 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. -- 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.
Re: [gmx-users] how many groups shall I use to control the temperature?
Thanks a lot, Justin. I do CG simulation using Martini force field. So maybe I can find some useful infomation on the forum of martini. Thanks :) From: Justin Lemkul Date: 2014-06-12 17:44 To: gmx-users Subject: Re: [gmx-users] how many groups shall I use to control the temperature? On 6/12/14, 2:37 AM, 陈功 wrote: Dear justin, I have doubts that whether I should use two groups to control the temperature or just one since there are just 604 hundred Protein beads and 6+ solvent beads. It is said that two groups are more accurate but when when i split them into two groups Protein nonProtein, I found that fluctulation of temperature in group Protein are obvious, Im afraid that would have an effect on accuracy on my simulation results. So how many groups shall I use to control the temperature? What protocol is used in published studies similar to what you're doing? Small groups will have larger fluctuations in temperature, that's a given. I don't do CG simulations, so I don't know how such groups are commonly treated. -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. -- 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] Acpyte with opls-aa
Dear users i wanted to know if Acpyte generated topologies for a ligand are compatible with OPLS-AA.ff? i am searching for a reliable topology builder for OPLS-aa like ATP for gromos53a6.ff so that i can avoid manual approached like using gaussian . regards, Saman---BeginMessage--- Dear users i wanted to know if Acpyte generated topologies for a ligand are compatible with OPLS-AA.ff? i am searching for a reliable topology builder for OPLS-aa like ATP for gromos53a6.ff so that i can avoid manual approached like using gaussian . regards, Saman---End Message--- -- 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] g_clustsize
On 2014-06-12 15:33, Raisa Kociurzynski wrote: Dear Prof. Van der Spoel, I want to calculate the clustersize of GM1 clusters in a DPPC membrane. I used g_clustersize but when I use the option -mol the index file is ignored and the whole system is used for the calculation. Is there any way to specify only GM1 molecules for the cluster calculation? I also tried to modify my xtc and tpr files, so that my system consists only of GM1 molecules, but then I only get one big cluster with g_clustsize. I could not find any solution for this problem in the gromacs forum. Best regards, Raisa Kociurzynski If you have a membrane there is only one cluster unless the membrane is fragmented into micelles. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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] -inf potential with TPIC
Hello Rafael, High energies (energy differences) are not discarded. When summing them through the exponential of their negative, they contribute very little to the final sum (lower energies dominate the sum). Hence, they are discarded. The -inf value on the mu standard error output is normal because, unlike the -tpi output, there is no ternary operator checking if the sum of exponentials is equal to zero (when it is, the log of zero gives you the inf value). The change to the double precision not giving you the -inf also makes sense, because the sum of exponentials, which on single-precision was zero, can now be non-zero due to the higher number of decimal places on double-precision. I am guessing with double-precision you are getting very high positive numbers (energies) for the mu, around 1000 maybe? My interpretation is that it is hard to find a favorable place to insert the water molecule in that cavity, at least with a few frames. I am guessing that with more and more frames, that may change, which is natural. I hope this has helped. Cheers, João On Thu, Jun 12, 2014 at 10:45 AM, Justin Lemkul jalem...@vt.edu wrote: On 6/11/14, 8:55 PM, Rafael I. Silverman y de la Vega wrote: I mistyped amber, when I should have typed charmm, amber is totally uninvolved in my calculations. I used the script from http://www.gromacs.org/Downloads/User_contributions/Other_software titled charmm2gromacs. The output looked fine after running it. And, I doubt its the cofactor, just ran the insertion with double precision mdrun, it gave reasonable looking results. There seems to be some sort of issue with unreasonable interaction energies not being discarded properly. It's entirely possible that there's something wrong with the tpic code; you can certainly file a bug report on Redmine with input files to reproduce it. -Justin On Tue, Jun 10, 2014 at 3:41 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/10/14, 6:14 PM, Rafael I. Silverman y de la Vega wrote: I meant that I only changed to cofactor to gromacs chamm27 format, not amber format. I used charmm27 for the apoprotein as well as the cofactor. What script did you use? I don't understand why Amber99SB is involved here, so I don't know exactly what you were doing to create the topology. It may not end up being useful information, but it's important to establish the validity of the underlying physical model. -Justin On Tue, Jun 10, 2014 at 3:09 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/10/14, 6:04 PM, Rafael I. Silverman y de la Vega wrote: you think it was the cofactor model? If you're using a CHARMM-parametrized cofactor with an Amber99SB protein, I'd say the simulations are wholly unreliable. It's certainly the #1 likely cause for nonsensical results. If you want to get to the root of the issue, you need to start with a solid foundation. Unless that's not what your last message meant? When you say only changed the cofactor, that implied to me that you didn't consistently convert everything in the system. -Justin On Tue, Jun 10, 2014 at 2:23 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/10/14, 5:01 PM, Rafael I. Silverman y de la Vega wrote: wait, I only changed the cofactor to gromacs charmm27.ff format Pretty amazing that the simulation even ran with that mash-up of parameters :) I'd say that's the most likely cause of your problems; nonsensical physical model leads to nonsensical output. -Justin On Tue, Jun 10, 2014 at 1:58 PM, Rafael I. Silverman y de la Vega rsilv...@ucsc.edu wrote: I suppose something might be wrong with the simulations. I am using gromacs 4.6.5, I am simulating a protein with a cofactor, someone else parametrized it, I changed from charmm to gromacs amber99sb.ff format with a script on the gromacs website. I did a typical em/nvt/npt equilibration followed by a 5 ns production run. I picked 250 frames out of the trajectory, and altered them to the TPIC input format with a script I wrote, to insert the particle half way between two atoms that I chose. I am inserting a water molecule. When I run the actual insertion some of the frames have a reasonable looking mu, and some have -inf mu. I think it may have to do with cavity size, some frames have too small of a cavity, so the interaction energy of the inserted water diverges... On Mon, Jun 9, 2014 at 6:40 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/9/14, 6:41 PM, Rafael I. Silverman y de la Vega wrote: Hi all, I am having a problem with -inf mu coming out of TPIC calculations. Anyone have some suggestions on how to avoid this? Tabulated potentials? Or can I modify the source code to reject the absurd values that cause this? I read a few old discussions on this, I didnt see much on how to handle this. I'd be much more concerned that something is going wrong in the simulations. I
[gmx-users] question about topolbuild
Dear gmxusers, I have a question about using topolbuild to generate topology for my ligand (intend to use OPLS AA forcefield). However, I am facing a problem in using the command, which according to the README text, requires the basic input as below topolbuild -n modelname -dir path_to_interp. -ff forcefield I have a ligand.mol2 and I typed in the command as below topolbuild1_3/src/topolbuild -n ligand -ff oplsaa -dir topolbuild1_3/dat/gromacs/ I got this error: Segmentation fault Could anyone helpme with this please? Thanks a lot. Best, HW -- 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] how many groups shall I use to control the temperature?
There is no rule regarding how many thermostats per system one needs. Often people choose separate thermostats for parts of system, which exhibit different mobility. I do not see any connection to functional forms of the interactions and, therefore, to force fields. Dr. Vitaly V. Chaban On Thu, Jun 12, 2014 at 2:33 PM, 陈功 gchen...@gmail.com wrote: Thanks a lot, Justin. I do CG simulation using Martini force field. So maybe I can find some useful infomation on the forum of martini. Thanks :) From: Justin Lemkul Date: 2014-06-12 17:44 To: gmx-users Subject: Re: [gmx-users] how many groups shall I use to control the temperature? On 6/12/14, 2:37 AM, 陈功 wrote: Dear justin, I have doubts that whether I should use two groups to control the temperature or just one since there are just 604 hundred Protein beads and 6+ solvent beads. It is said that two groups are more accurate but when when i split them into two groups Protein nonProtein, I found that fluctulation of temperature in group Protein are obvious, Im afraid that would have an effect on accuracy on my simulation results. So how many groups shall I use to control the temperature? What protocol is used in published studies similar to what you're doing? Small groups will have larger fluctuations in temperature, that's a given. I don't do CG simulations, so I don't know how such groups are commonly treated. -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. -- 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.
Re: [gmx-users] Interaction energy between helices
On 6/12/14, 2:02 PM, Natalia Alveal F. wrote: Thanks Justin, but for how long do this new simulation? It's not a new simulation. You're re-processing your existing trajectory. Usually the energy evaluations only take a few minutes. The practical impact of energygrps during a run is usually fairly insignificant, but that's also a function of how many groups there are and how often you're writing to disk. -Justin Natalia 2014-06-11 18:14 GMT-04:00 Justin Lemkul jalem...@vt.edu: On 6/11/14, 5:36 PM, Natalia Alveal F. wrote: Dear Gromacs users, I want to calculate the energy of interaction between two helices of a protein, but g_energy dont have the option for -ndx file to select these specific residues of a helix. How I can do this? That's what energygrps in the .mdp file are for. Re-calculate the energies with mdrun -rerun using the new .tpr file. -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. -- == 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] Adding residue at two end of DNA
Dear Gromacs User, Do you know how can I add some residue to ends of DNA? I am looking forward hearing of you,= Mahdi Bagherpoor -- 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] hardware problem of GPU?
thanks a lot. Finally both GPU are working. Albert On 06/11/2014 01:21 PM, Mark Abraham wrote: This is not a hardware issue. See http://www.gromacs.org/Documentation/Acceleration_and_parallelization#Heterogenous_parallelization.3a_using_GPUs Mark -- 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] Using specbond.dat in pdb2gmx
On 6/11/14, 2:33 PM, Matthew Stancea wrote: ? Hello, I have been having a bit of issues generating an accurate gromacs topology file (topol.top) utilizing a pdb of a cyclic peptide in pdb2gmx. I have been able to generate topologies that are almost identical to the original pdb using the option -ignh at the end of my command, but doing so deletes the bond between the first nitrogen and the last carbon (which should be connected for this peptide to be cyclic) and adds two additional hydrogens and a positive charge to the first nitrogen and an additional oxygen and a negative charge to the last carbon, rendering this peptide as non-cyclic. After searching around for quite a while, I found out that many others on this mailing list were having the same issues as myself, and some replies to their messages including the usage of a file known as specbond.dat which may be helpful in retaining that bond. The -ignh flag is not relevant to those observations. In my working directory, I have a file named specbond.dat and it contains the following information: 3 CYS N 1 VAL C 1 0.25CYS2VAL2 CYS SG 1 CYS SG 1 0.25CYS2CYS2 CYM SG 1 CYM SG 1 0.25CYS2CYS2 When I input the command pdb2gmx_mpi -ff amber99sb -water tip3p -f 1NB1.pdb -o conf.gro -p topol.top -i kalata.itp while specbond.dat is in the working directory (Here is a link for the structure of peptide 1NB1 for reference if needed: http://www.ncbi.nlm.nih.gov/protein/1NB1_A ), I get the following message: --- Program pdb2gmx_mpi, VERSION 4.6.2 Source code file: /home/msaum/apps/gromacs-4.6.2/src/kernel/pdb2gmx.c, line: 727 Fatal error: Atom HB3 in residue CYS 1 was not found in rtp entry NCYS with 13 atoms while sorting atoms. For a hydrogen, this can be a different protonation state, or it might have had a different number in the PDB file and was rebuilt (it might for instance have been H3, and we only expected H1 H2). Note that hydrogens might have been added to the entry for the N-terminus. Remove this hydrogen or choose a different protonation state to solve it. Option -ignh will ignore all hydrogens in the input. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- (HB3 would be the hydrogen of a cysteine residue that has not formed a disulfide bond with another amino acid residue, however my pdb does not contain an HB3). I then tried adding -ignh as per the suggestion in the twelfth line in that message. The following is a part of the message I received: Checking for duplicate atoms Generating any missing hydrogen atoms and/or adding termini. Now there are 29 residues with 385 atoms Making bonds... Number of bonds was 390, now 389 Generating angles, dihedrals and pairs... Before cleaning: 1010 pairs Before cleaning: 1030 dihedrals Keeping all generated dihedrals Making cmap torsions...There are 1030 dihedrals, 73 impropers, 699 angles 1007 pairs, 389 bonds and 0 virtual sites Total mass 2916.376 a.m.u. Total charge -0.000 e Writing topology Writing coordinate file... - PLEASE NOTE You have successfully generated a topology from: 1NB1.pdb. The Amber99sb force field and the tip3p water model are used. - ETON ESAELP On the fifth line of that excerpt, I read Number of bonds was 390, now 389 and questioned what that could mean. Because of that, I wanted to verify that the topology that was successfully generated contains all the necessary bonds, so I looked through the topol.top file and saw 3 total hydrogens on the terminal nitrogen on the beginning cysteine and two total oxygens on the terminal carbon on the ending valine. Also, I did not see a bond between that nitrogen and that carbon (atoms 1 and 383); these data lead me to believe that this peptide is no longer cyclic. Construction of termini and assignment of ionization state is done with -ter. For your case, you likely need to be using -ter and selecting None. When I input the command pdb2gmx_mpi -ff amber99sb -water tip3p -f 1NB1.pdb -o conf.gro -p topol.top -i kalata.itp -ter, I received the same message as before without any kind of interactivity for selecting options. Because of this, I tried the command pdb2gmx_mpi -ff amber99sb -water tip3p -f 1NB1.pdb -o conf.gro -p topol.top -i kalata.itp -inter -ter, which asked about the protonation of residue 24 (arginine), and when I answer none, I get this message: Processing chain 1 'A' (376 atoms, 29 residues) Which ARGININE type do you want for residue 24 0. Not protonated (charge 0) (-) 1. Protonated (charge +1) (ARG) Type a number:none --- Program
Re: [gmx-users] Using specbond.dat in pdb2gmx
On 6/12/14, 4:53 PM, Matthew Stancea wrote: On 6/11/14, 2:33 PM, Matthew Stancea wrote: ? Hello, I have been having a bit of issues generating an accurate gromacs topology file (topol.top) utilizing a pdb of a cyclic peptide in pdb2gmx. I have been able to generate topologies that are almost identical to the original pdb using the option -ignh at the end of my command, but doing so deletes the bond between the first nitrogen and the last carbon (which should be connected for this peptide to be cyclic) and adds two additional hydrogens and a positive charge to the first nitrogen and an additional oxygen and a negative charge to the last carbon, rendering this peptide as non-cyclic. After searching around for quite a while, I found out that many others on this mailing list were having the same issues as myself, and some replies to their messages including the usage of a file known as specbond.dat which may be helpful in retaining that bond. The -ignh flag is not relevant to those observations. In my working directory, I have a file named specbond.dat and it contains the following information: 3 CYS N 1 VAL C 1 0.25CYS2VAL2 CYS SG 1 CYS SG 1 0.25CYS2CYS2 CYM SG 1 CYM SG 1 0.25CYS2CYS2 When I input the command pdb2gmx_mpi -ff amber99sb -water tip3p -f 1NB1.pdb -o conf.gro -p topol.top -i kalata.itp while specbond.dat is in the working directory (Here is a link for the structure of peptide 1NB1 for reference if needed: http://www.ncbi.nlm.nih.gov/protein/1NB1_A ), I get the following message: --- Program pdb2gmx_mpi, VERSION 4.6.2 Source code file: /home/msaum/apps/gromacs-4.6.2/src/kernel/pdb2gmx.c, line: 727 Fatal error: Atom HB3 in residue CYS 1 was not found in rtp entry NCYS with 13 atoms while sorting atoms. For a hydrogen, this can be a different protonation state, or it might have had a different number in the PDB file and was rebuilt (it might for instance have been H3, and we only expected H1 H2). Note that hydrogens might have been added to the entry for the N-terminus. Remove this hydrogen or choose a different protonation state to solve it. Option -ignh will ignore all hydrogens in the input. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- (HB3 would be the hydrogen of a cysteine residue that has not formed a disulfide bond with another amino acid residue, however my pdb does not contain an HB3). I then tried adding -ignh as per the suggestion in the twelfth line in that message. The following is a part of the message I received: Checking for duplicate atoms Generating any missing hydrogen atoms and/or adding termini. Now there are 29 residues with 385 atoms Making bonds... Number of bonds was 390, now 389 Generating angles, dihedrals and pairs... Before cleaning: 1010 pairs Before cleaning: 1030 dihedrals Keeping all generated dihedrals Making cmap torsions...There are 1030 dihedrals, 73 impropers, 699 angles 1007 pairs, 389 bonds and 0 virtual sites Total mass 2916.376 a.m.u. Total charge -0.000 e Writing topology Writing coordinate file... - PLEASE NOTE You have successfully generated a topology from: 1NB1.pdb. The Amber99sb force field and the tip3p water model are used. - ETON ESAELP On the fifth line of that excerpt, I read Number of bonds was 390, now 389 and questioned what that could mean. Because of that, I wanted to verify that the topology that was successfully generated contains all the necessary bonds, so I looked through the topol.top file and saw 3 total hydrogens on the terminal nitrogen on the beginning cysteine and two total oxygens on the terminal carbon on the ending valine. Also, I did not see a bond between that nitrogen and that carbon (atoms 1 and 383); these data lead me to believe that this peptide is no longer cyclic. This is related to removing duplicate bonds after merging .rtp and .tdb entries. It's normal output; there are almost always duplicates. Construction of termini and assignment of ionization state is done with -ter. For your case, you likely need to be using -ter and selecting None. When I input the command pdb2gmx_mpi -ff amber99sb -water tip3p -f 1NB1.pdb -o conf.gro -p topol.top -i kalata.itp -ter, I received the same message as before without any kind of interactivity for selecting options. Because of this, I tried the command pdb2gmx_mpi -ff amber99sb -water tip3p -f 1NB1.pdb -o conf.gro -p topol.top -i kalata.itp -inter -ter, which asked about the protonation of residue 24 (arginine), and when I answer none, I get this message: Processing chain 1 'A' (376 atoms, 29 residues) Which ARGININE type
[gmx-users] about thermal intergation calculations
Hi All: I am trying to do free energy calculations by thermal integration method and I have read the tutorials on the gromacs web site, they are really nice tutorials and help me a lot. But I still have two questions here: 1, After we define the necessary paramteres in the mdp file (such as the lambda values), when we run MD simulation using these mdp files, we get a file (default name dhdl.xvg) of the derivatives of Hamilton relative to the lambda values (the dH/dLAMBDA) as a function of simulation time, and the free energy difference is the integration of this value, right? My question is, how does this value calculated? Since in the simulations, we modified some interactions by using a specific lambda value, I can understand how to calculate the Hamilton or energy of the system under this specific lambda value, but how does the derivatives of Hamilton calculated? 2, General we use different lambda to modify the vdw or electrostatic interactions between ligand and it's environment, i understand how this work in gromacs. However, I am planning to restrain distances between specific atoms and use different lambda to change the equilibrium distances between these atoms. Is there any code implemented in gromacs to do this? Or I need to run simulations at each lambda value and calculated the potential energy as well as the derivatives and integrations by myself? Thanks very much for your help! RXG -- 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] Why does the list keep unsubscribing me?
Hi Mark, Thanks for your email. Firstly we don't even know if the exact problem is. It is just an assumption that this is happening. I understand that maybe I am the only one (or maybe others never got reported). Its just my attitude to try to remove bugs when I find and not wait for enough incidents to happen, but that might just be difference of opinions. PS. A quick look at Mailman http://www.list.org/mailman-member/node41.html; tells that confirmation options do exist in Mailman for unsubscribe and it has to be switched on (in fact it seems confirmation is by default, but GROMACS mailman at KTH has been configured otherwise). But again, I understand that for just a single case, it might to too much work to do. Have a nice day,cheers,Abhi Date: Thu, 12 Jun 2014 13:57:12 +0200 From: mark.j.abra...@gmail.com To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Why does the list keep unsubscribing me? Hi, I've no idea if mailman even has that option, or the KTH IT admins would be willing to set it up, but that's not worth exploring until automatic unsubscription is known to be a problem for more than one email address. Mark On Thu, Jun 12, 2014 at 1:34 PM, X Rules xru...@live.com wrote: Thanks for the solution Mark, but from what I feel the right way to do is to fix mailman (add another option of clicking a link sent to your email to confirm unsubscribe, the same way subscription works). I might not be the only one, or may be I am the only one complaining :). Lets see how long this lasts,Abhi Date: Thu, 12 Jun 2014 10:22:48 +0200 From: mark.j.abra...@gmail.com To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Why does the list keep unsubscribing me? Hi, One simple solution is to subscribe with a different email address. Mark On Thu, Jun 12, 2014 at 9:54 AM, X Rules xru...@live.com wrote: This is the 4th time I am thrown out of the list by some random phishing email and I am done with this. If I am thrown out this time (I know I will be and no-one cares to fix any issues), I am not coming back. I just came back the last time to thank you folks for all your comments and helps regarding gromacs.have fun !! From: xru...@live.com To: gmx-us...@gromacs.org Date: Mon, 2 Jun 2014 04:16:24 + Subject: 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
