Re: [gmx-users] Regarding membrane construction
On 6/11/14, 6:25 AM, Venkat Reddy wrote: Dear Justin, I am following membrane-protein tutorial to construct my system. During equilibration and production MD, I am receiving the following NOTES. NOTE 1 [file md.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy NOTE 2 [file md.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 I have downloaded the mdp files from tutorial. Is it ok if I omit these notes and carry the production run? Notes are just for informative purposes. Warnings indicate problems. -Justin On Tue, Jun 10, 2014 at 5:41 PM, Justin Lemkul wrote: On 6/10/14, 1:12 AM, Venkat Reddy wrote: I have used editconf -f protein.gro -c -bt cubic -d 1.5 -o confout.gro to set the box. Then genbox -cp confout.gro -cs dppc128.gro -o protein_in_membrane.gro got hanged Am I missing something here??? Don't extend the z-dimension at this stage. You want to expand the membrane laterally (along x and y, usually), so set the box vectors manually with editconf -box, not -d (though using -d can tell you what suitable vectors in x and y might be). You can always increase the z-dimension, if you need to, later using editconf and then fill with water using genbox in a separate step. -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.
Re: [gmx-users] Regarding membrane construction
Dear Justin, I am following membrane-protein tutorial to construct my system. During equilibration and production MD, I am receiving the following NOTES. NOTE 1 [file md.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy NOTE 2 [file md.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 I have downloaded the mdp files from tutorial. Is it ok if I omit these notes and carry the production run? On Tue, Jun 10, 2014 at 5:41 PM, Justin Lemkul wrote: > > > On 6/10/14, 1:12 AM, Venkat Reddy wrote: > >> I have used >> editconf -f protein.gro -c -bt cubic -d 1.5 -o confout.gro >> to set the box. >> >> Then >> genbox -cp confout.gro -cs dppc128.gro -o protein_in_membrane.gro >> got hanged >> >> >> Am I missing something here??? >> > > Don't extend the z-dimension at this stage. You want to expand the > membrane laterally (along x and y, usually), so set the box vectors > manually with editconf -box, not -d (though using -d can tell you what > suitable vectors in x and y might be). You can always increase the > z-dimension, if you need to, later using editconf and then fill with water > using genbox in a separate step. > > > -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. > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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] Regarding membrane construction
On 6/10/14, 1:12 AM, Venkat Reddy wrote: I have used editconf -f protein.gro -c -bt cubic -d 1.5 -o confout.gro to set the box. Then genbox -cp confout.gro -cs dppc128.gro -o protein_in_membrane.gro got hanged Am I missing something here??? Don't extend the z-dimension at this stage. You want to expand the membrane laterally (along x and y, usually), so set the box vectors manually with editconf -box, not -d (though using -d can tell you what suitable vectors in x and y might be). You can always increase the z-dimension, if you need to, later using editconf and then fill with water using genbox in a separate step. -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] Regarding membrane construction
I have used editconf -f protein.gro -c -bt cubic -d 1.5 -o confout.gro to set the box. Then genbox -cp confout.gro -cs dppc128.gro -o protein_in_membrane.gro got hanged Am I missing something here??? On Tue, Jun 10, 2014 at 2:51 AM, Justin Lemkul wrote: > > > On 6/9/14, 9:08 AM, Venkat Reddy wrote: > >> Dear Justin, >> I have tried the command >> genbox -cp protein.gro -cs membrane.gro -o protein_in_membrane.gro >> but it got hanged. Is there something wrong with the command? >> >> > I wouldn't expect a hang as long as the box is set to appropriate > dimensions. The new box for the protein shouldn't be substantially larger > than the membrane itself. > > > -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. > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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] Regarding membrane construction
On 6/9/14, 9:08 AM, Venkat Reddy wrote: Dear Justin, I have tried the command genbox -cp protein.gro -cs membrane.gro -o protein_in_membrane.gro but it got hanged. Is there something wrong with the command? I wouldn't expect a hang as long as the box is set to appropriate dimensions. The new box for the protein shouldn't be substantially larger than the membrane itself. -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] Regarding membrane construction
Dear Justin, I have tried the command genbox -cp protein.gro -cs membrane.gro -o protein_in_membrane.gro but it got hanged. Is there something wrong with the command? On Mon, Jun 9, 2014 at 5:50 PM, 陈功 wrote: > Thanks for correction. i appriciate it :) > Chen Gong > > > > > > From: Justin Lemkul > Date: 2014-06-09 19:58 > To: gmx-users > Subject: Re: [gmx-users] Regarding membrane construction > > > On 6/9/14, 3:22 AM, 陈功 wrote: > > Dear Venkat, I guess there are some other methods to generate new lipid > > bilayer construct by using genbox -cp your_membrane_protein -ci > lipid_monomer > > -nmol xxxcalculate by yourself -try 1000 -cs solovents.gro -p top.top -o > > new_conf.gro or using editconf & cat ...Another way, you can try the > script > > packmol. Be more patient. haha, I m also a new gmx user. Good luck, > chen > > Packmol is a good choice, but the approach above with genbox likely won't > work. > It will produce a random insertion of lipids. The simplest way within > Gromacs > to create a membrane of sufficient size is to place the protein in a > suitably > sized box (with editconf) and then > > genbox -cp protein.gro -cs membrane.gro -o protein_in_membrane.gro > > -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. > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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] Regarding membrane construction
Thanks for correction. i appriciate it :) Chen Gong From: Justin Lemkul Date: 2014-06-09 19:58 To: gmx-users Subject: Re: [gmx-users] Regarding membrane construction On 6/9/14, 3:22 AM, 陈功 wrote: > Dear Venkat, I guess there are some other methods to generate new lipid > bilayer construct by using genbox -cp your_membrane_protein -ci lipid_monomer > -nmol xxxcalculate by yourself -try 1000 -cs solovents.gro -p top.top -o > new_conf.gro or using editconf & cat ...Another way, you can try the script > packmol. Be more patient. haha, I m also a new gmx user. Good luck, chen Packmol is a good choice, but the approach above with genbox likely won't work. It will produce a random insertion of lipids. The simplest way within Gromacs to create a membrane of sufficient size is to place the protein in a suitably sized box (with editconf) and then genbox -cp protein.gro -cs membrane.gro -o protein_in_membrane.gro -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] Regarding membrane construction
Thank you Justin. On Mon, Jun 9, 2014 at 5:28 PM, Justin Lemkul wrote: > > > On 6/9/14, 3:22 AM, 陈功 wrote: > >> Dear Venkat, I guess there are some other methods to generate new lipid >> bilayer construct by using genbox -cp your_membrane_protein -ci >> lipid_monomer >> -nmol xxxcalculate by yourself -try 1000 -cs solovents.gro -p top.top -o >> new_conf.gro or using editconf & cat ...Another way, you can try the >> script >> packmol. Be more patient. haha, I m also a new gmx user. Good luck, chen >> > > Packmol is a good choice, but the approach above with genbox likely won't > work. It will produce a random insertion of lipids. The simplest way > within Gromacs to create a membrane of sufficient size is to place the > protein in a suitably sized box (with editconf) and then > > genbox -cp protein.gro -cs membrane.gro -o protein_in_membrane.gro > > -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. > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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] Regarding membrane construction
On 6/9/14, 3:22 AM, 陈功 wrote: Dear Venkat, I guess there are some other methods to generate new lipid bilayer construct by using genbox -cp your_membrane_protein -ci lipid_monomer -nmol xxxcalculate by yourself -try 1000 -cs solovents.gro -p top.top -o new_conf.gro or using editconf & cat ...Another way, you can try the script packmol. Be more patient. haha, I m also a new gmx user. Good luck, chen Packmol is a good choice, but the approach above with genbox likely won't work. It will produce a random insertion of lipids. The simplest way within Gromacs to create a membrane of sufficient size is to place the protein in a suitably sized box (with editconf) and then genbox -cp protein.gro -cs membrane.gro -o protein_in_membrane.gro -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] Regarding membrane construction
Thank you Chen for the quick reply. I will try both options. On Mon, Jun 9, 2014 at 12:52 PM, 陈功 wrote: > Dear Venkat, > I guess there are some other methods to generate new lipid bilayer > construct by using genbox -cp your_membrane_protein -ci lipid_monomer -nmol > xxxcalculate by yourself -try 1000 -cs solovents.gro -p top.top -o > new_conf.gro or using editconf & cat ...Another way, you can try the script > packmol. Be more patient. haha, I m also a new gmx user. > Good luck, > chen gong > > > > > > > From: Venkat Reddy > Date: 2014-06-09 15:31 > To: Discussion list for GROMACS users > Subject: [gmx-users] Regarding membrane construction > Dear all, > I am studying a membrane protein of length 288 residues. I want to simulate > in a DPPC bilayer. I have downloaded dppc equilibrated bilayer from Peter > Tieleman's website as directed by Justin in his membrane-protein tutorial. > But I found 128 lipid membrane is not enough for my protein. From the > literature, I found I need 81 lipids in each leaflet. How can I construct > a 162 lipid equilibrated bilayer? I tried CHARMM-GUI to build it. But the > equilibration is giving RATTLE error. Please help me in this regard. > > Thank you > > Venkat > -- > 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. > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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] Regarding membrane construction
Dear Venkat, I guess there are some other methods to generate new lipid bilayer construct by using genbox -cp your_membrane_protein -ci lipid_monomer -nmol xxxcalculate by yourself -try 1000 -cs solovents.gro -p top.top -o new_conf.gro or using editconf & cat ...Another way, you can try the script packmol. Be more patient. haha, I m also a new gmx user. Good luck, chen gong From: Venkat Reddy Date: 2014-06-09 15:31 To: Discussion list for GROMACS users Subject: [gmx-users] Regarding membrane construction Dear all, I am studying a membrane protein of length 288 residues. I want to simulate in a DPPC bilayer. I have downloaded dppc equilibrated bilayer from Peter Tieleman's website as directed by Justin in his membrane-protein tutorial. But I found 128 lipid membrane is not enough for my protein. From the literature, I found I need 81 lipids in each leaflet. How can I construct a 162 lipid equilibrated bilayer? I tried CHARMM-GUI to build it. But the equilibration is giving RATTLE error. Please help me in this regard. Thank you Venkat -- 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] Regarding membrane construction
Dear all, I am studying a membrane protein of length 288 residues. I want to simulate in a DPPC bilayer. I have downloaded dppc equilibrated bilayer from Peter Tieleman's website as directed by Justin in his membrane-protein tutorial. But I found 128 lipid membrane is not enough for my protein. From the literature, I found I need 81 lipids in each leaflet. How can I construct a 162 lipid equilibrated bilayer? I tried CHARMM-GUI to build it. But the equilibration is giving RATTLE error. Please help me in this regard. Thank you Venkat -- 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.
