Re: [gmx-users] Drude force field
On 7/20/19 12:26 AM, Myunggi Yi wrote: Dear Justin, I've followed the instructions, and I prepared my system. I've got the following error message. " No default Bond types." There are several errors. The bond is between atoms 43 and 45, and the following is a part of the dmpc.itp, which is generated by pdb2gmx with drude-2013f_2018_10.ff 43 OD30CL 1 DMPCO21 43 1.484715.5994 ; qtot 1.803 44 DRUD 1 DMPC DO21 44-1.4847 0 ; qtot 0.318 45LPD 1 DMPC LPMA 45 -0.17 0 ; qtot 0.148 46LPD 1 DMPC LPMB 46 -0.17 0 ; qtot -0.022 47 CD2O3B 1 DMPCC21 472.72816 11.611 ; qtot 2.706 48 DRUD 1 DMPC DC21 48 -2.03116 0 ; qtot 0.675 It seems gromacs added a bond to them, which is not available in the dmpc.itp file. Is it common the bond between polar heavy atom and the lone pair virtual sites? There should be no bonds to lone pairs. It seems there is an error in the .rtp entry for the lipid. The conversion script I used explicitly removes these but clearly there is some kind of bug that's not catching this. I will look into it. For now, simply remove any LP references in [bonds] and regenerate the topology. Program information: GROMACS: gmx grompp, version 2016-dev-20181220-a2cab74 Command line: gmx grompp -f em.mdp -c ../gg.gro -r ../gg.gro -p ../topol.top -o em.tpr In addition, I do have not integer total charge. NOTE 2 [file topol.top, line 49]: System has non-zero total charge: -0.000464 Of course, when I generate the protein itp, the total charge was 0.00. As you know DMPC is neutral too. After combine protein, dmpc, water, this happened. That's just rounding error. You're going to encounter this a lot due to the large number of fractionally charged particles in a polarizable system. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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] Drude force field
Dear Justin, I've followed the instructions, and I prepared my system. I've got the following error message. " No default Bond types." There are several errors. The bond is between atoms 43 and 45, and the following is a part of the dmpc.itp, which is generated by pdb2gmx with drude-2013f_2018_10.ff 43 OD30CL 1 DMPCO21 43 1.484715.5994 ; qtot 1.803 44 DRUD 1 DMPC DO21 44-1.4847 0 ; qtot 0.318 45LPD 1 DMPC LPMA 45 -0.17 0 ; qtot 0.148 46LPD 1 DMPC LPMB 46 -0.17 0 ; qtot -0.022 47 CD2O3B 1 DMPCC21 472.72816 11.611 ; qtot 2.706 48 DRUD 1 DMPC DC21 48 -2.03116 0 ; qtot 0.675 It seems gromacs added a bond to them, which is not available in the dmpc.itp file. Is it common the bond between polar heavy atom and the lone pair virtual sites? Program information: GROMACS: gmx grompp, version 2016-dev-20181220-a2cab74 Command line: gmx grompp -f em.mdp -c ../gg.gro -r ../gg.gro -p ../topol.top -o em.tpr In addition, I do have not integer total charge. NOTE 2 [file topol.top, line 49]: System has non-zero total charge: -0.000464 Of course, when I generate the protein itp, the total charge was 0.00. As you know DMPC is neutral too. After combine protein, dmpc, water, this happened. Any suggestion? Thank you. On Thu, Jul 18, 2019 at 11:22 AM Justin Lemkul wrote: > On Wed, Jul 17, 2019 at 8:58 PM Myunggi Yi wrote: > > > Thank you Dr. Lemkel, > > > > I don't have ions in my simulation. It's a neutral system with a protein > in > > membrane bilayer with solvent. > > I have downloaded the force field (Drude FF for charmm FF in Gromacs > > format). to run the simulation with charmm FF in "Gromacs 2019.3". > > However, it seems the format of the file does not match with the current > > version. > > > > In the web, > > > > Compile and install as you would any other (post-5.0) GROMACS version. If > > you attempt to use *ANY OTHER VERSION OF GROMACS, the Drude features will > > not be accessible.* > > > > There are 5.0 and 5.1 series of Gromacs versions. Which one should I use? > > > > Or, it there a way to modify the force field format to use the current > > version of Gromacs?, Then I will modify the format. > > > > > Read the information at the previous link more carefully. You cannot use > any released version of GROMACS. You must use the developmental version as > instructed in that link. > > -Justin > > > > > > On Thu, Jul 18, 2019 at 9:43 AM Justin Lemkul wrote: > > > > > > > > > > > On 7/17/19 8:39 PM, Myunggi Yi wrote: > > > > Dear users, > > > > > > > > I want to run a simulation with a polarizable force field. > > > > > > > > How and where can I get Drude force field for the current version of > > > > Gromacs? > > > > > > Everything you need to know: > > > > > > http://mackerell.umaryland.edu/charmm_drude_ff.shtml > > > > > > The implementation is not complete. If your system has ions, do not use > > > GROMACS due to the lack of NBTHOLE. In that case, use NAMD, CHARMM, or > > > OpenMM. The Drude model is still considered experimental, hence it is > > > not officially supported yet. There have been a lot of snags along the > > > way (mostly in my time to get the code up to par for official > inclusion). > > > > > > -Justin > > > > > > -- > > > == > > > > > > Justin A. Lemkul, Ph.D. > > > Assistant Professor > > > Office: 301 Fralin Hall > > > Lab: 303 Engel Hall > > > > > > Virginia Tech Department of Biochemistry > > > 340 West Campus Dr. > > > Blacksburg, VA 24061 > > > > > > jalem...@vt.edu | (540) 231-3129 > > > http://www.thelemkullab.com > > > > > > == > > > > > > -- > > > 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. > > > -- > > == > > Justin A. Lemkul, Ph.D. > > Assistant Professor > > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemku
Re: [gmx-users] Drude force field
On Thu, Jul 18, 2019 at 4:23 AM Gordan Horvat wrote: > I have found this in the NAMD manual: > > NAMD has the ability to load GROMACS ASCII topology (.top) and > coordinate (.gro) files, which allows you to run most GROMACS > simulations in NAMD. > http://www.ks.uiuc.edu/Research/namd/2.9/ug/node14.html > > Is that applicable to the Drude input files prepared by the Gromacs > Drude distribution? > No. To do Drude polarizable simulations in NAMD, you need a CHARMM PSF. -Justin > Gordan > > -- > Gordan Horvat > Division of Physical Chemistry > Department of Chemistry > Faculty of Science, University of Zagreb > Croatia > > On 18.7.2019. 08:33, gromacs.org_gmx-users-requ...@maillist.sys.kth.se > wrote: > > On Wed, Jul 17, 2019 at 8:58 PM Myunggi Yi > wrote: > > > >> >Thank you Dr. Lemkel, > >> > > >> >I don't have ions in my simulation. It's a neutral system with a > protein in > >> >membrane bilayer with solvent. > >> >I have downloaded the force field (Drude FF for charmm FF in Gromacs > >> >format). to run the simulation with charmm FF in "Gromacs 2019.3". > >> >However, it seems the format of the file does not match with the > current > >> >version. > >> > > >> >In the web, > >> > > >> >Compile and install as you would any other (post-5.0) GROMACS version. > If > >> >you attempt to use *ANY OTHER VERSION OF GROMACS, the Drude features > will > >> >not be accessible.* > >> > > >> >There are 5.0 and 5.1 series of Gromacs versions. Which one should I > use? > >> > > >> >Or, it there a way to modify the force field format to use the current > >> >version of Gromacs?, Then I will modify the format. > >> > > >> > > > Read the information at the previous link more carefully. You cannot use > > any released version of GROMACS. You must use the developmental version > as > > instructed in that link. > > > > -Justin > > > > > >> > > >> >On Thu, Jul 18, 2019 at 9:43 AM Justin Lemkul wrote: > >> > > >>> > > > >>> > > > >>> > >On 7/17/19 8:39 PM, Myunggi Yi wrote: > > > >Dear users, > > > > > > > >I want to run a simulation with a polarizable force field. > > > > > > > >How and where can I get Drude force field for the current > version of > > > >Gromacs? > >>> > > > >>> > >Everything you need to know: > >>> > > > >>> > >http://mackerell.umaryland.edu/charmm_drude_ff.shtml > >>> > > > >>> > >The implementation is not complete. If your system has ions, do not > use > >>> > >GROMACS due to the lack of NBTHOLE. In that case, use NAMD, CHARMM, > or > >>> > >OpenMM. The Drude model is still considered experimental, hence it > is > >>> > >not officially supported yet. There have been a lot of snags along > the > >>> > >way (mostly in my time to get the code up to par for official > inclusion). > >>> > > > >>> > >-Justin > >>> > > > >>> > >-- > >>> > >== > >>> > > > >>> > >Justin A. Lemkul, Ph.D. > >>> > >Assistant Professor > >>> > >Office: 301 Fralin Hall > >>> > >Lab: 303 Engel Hall > >>> > > > >>> > >Virginia Tech Department of Biochemistry > >>> > >340 West Campus Dr. > >>> > >Blacksburg, VA 24061 > >>> > > > >>> > >jalem...@vt.edu | (540) 231-3129 > >>> > >http://www.thelemkullab.com > >>> > > > >>> > >== > >>> > > > >>> > >-- > >>> > >Gromacs Users mailing list > >>> > > > >>> > >* Please search the archive at > >>> > >http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >>> > >posting! > >>> > > > >>> > >* Can't post? Readhttp://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 togmx-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? Readhttp://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 togmx-users-requ...@gromacs.org. > >> > > > -- == Justin A. Lemkul, Ph.D. > > Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry 340 West Campus Dr. > > Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 > > http://www.thelemkullab.com == > > > -- > 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. A
Re: [gmx-users] Drude force field
I have found this in the NAMD manual: NAMD has the ability to load GROMACS ASCII topology (.top) and coordinate (.gro) files, which allows you to run most GROMACS simulations in NAMD. http://www.ks.uiuc.edu/Research/namd/2.9/ug/node14.html Is that applicable to the Drude input files prepared by the Gromacs Drude distribution? Gordan -- Gordan Horvat Division of Physical Chemistry Department of Chemistry Faculty of Science, University of Zagreb Croatia On 18.7.2019. 08:33, gromacs.org_gmx-users-requ...@maillist.sys.kth.se wrote: On Wed, Jul 17, 2019 at 8:58 PM Myunggi Yi wrote: >Thank you Dr. Lemkel, > >I don't have ions in my simulation. It's a neutral system with a protein in >membrane bilayer with solvent. >I have downloaded the force field (Drude FF for charmm FF in Gromacs >format). to run the simulation with charmm FF in "Gromacs 2019.3". >However, it seems the format of the file does not match with the current >version. > >In the web, > >Compile and install as you would any other (post-5.0) GROMACS version. If >you attempt to use *ANY OTHER VERSION OF GROMACS, the Drude features will >not be accessible.* > >There are 5.0 and 5.1 series of Gromacs versions. Which one should I use? > >Or, it there a way to modify the force field format to use the current >version of Gromacs?, Then I will modify the format. > > Read the information at the previous link more carefully. You cannot use any released version of GROMACS. You must use the developmental version as instructed in that link. -Justin > >On Thu, Jul 18, 2019 at 9:43 AM Justin Lemkul wrote: > > > > > > >On 7/17/19 8:39 PM, Myunggi Yi wrote: > > >Dear users, > > > > > >I want to run a simulation with a polarizable force field. > > > > > >How and where can I get Drude force field for the current version of > > >Gromacs? > > > >Everything you need to know: > > > >http://mackerell.umaryland.edu/charmm_drude_ff.shtml > > > >The implementation is not complete. If your system has ions, do not use > >GROMACS due to the lack of NBTHOLE. In that case, use NAMD, CHARMM, or > >OpenMM. The Drude model is still considered experimental, hence it is > >not officially supported yet. There have been a lot of snags along the > >way (mostly in my time to get the code up to par for official inclusion). > > > >-Justin > > > >-- > >== > > > >Justin A. Lemkul, Ph.D. > >Assistant Professor > >Office: 301 Fralin Hall > >Lab: 303 Engel Hall > > > >Virginia Tech Department of Biochemistry > >340 West Campus Dr. > >Blacksburg, VA 24061 > > > >jalem...@vt.edu | (540) 231-3129 > >http://www.thelemkullab.com > > > >== > > > >-- > >Gromacs Users mailing list > > > >* Please search the archive at > >http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >posting! > > > >* Can't post? Readhttp://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 togmx-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? Readhttp://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 togmx-users-requ...@gromacs.org. > -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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] Drude force field
On Wed, Jul 17, 2019 at 8:58 PM Myunggi Yi wrote: > Thank you Dr. Lemkel, > > I don't have ions in my simulation. It's a neutral system with a protein in > membrane bilayer with solvent. > I have downloaded the force field (Drude FF for charmm FF in Gromacs > format). to run the simulation with charmm FF in "Gromacs 2019.3". > However, it seems the format of the file does not match with the current > version. > > In the web, > > Compile and install as you would any other (post-5.0) GROMACS version. If > you attempt to use *ANY OTHER VERSION OF GROMACS, the Drude features will > not be accessible.* > > There are 5.0 and 5.1 series of Gromacs versions. Which one should I use? > > Or, it there a way to modify the force field format to use the current > version of Gromacs?, Then I will modify the format. > > Read the information at the previous link more carefully. You cannot use any released version of GROMACS. You must use the developmental version as instructed in that link. -Justin > > On Thu, Jul 18, 2019 at 9:43 AM Justin Lemkul wrote: > > > > > > > On 7/17/19 8:39 PM, Myunggi Yi wrote: > > > Dear users, > > > > > > I want to run a simulation with a polarizable force field. > > > > > > How and where can I get Drude force field for the current version of > > > Gromacs? > > > > Everything you need to know: > > > > http://mackerell.umaryland.edu/charmm_drude_ff.shtml > > > > The implementation is not complete. If your system has ions, do not use > > GROMACS due to the lack of NBTHOLE. In that case, use NAMD, CHARMM, or > > OpenMM. The Drude model is still considered experimental, hence it is > > not officially supported yet. There have been a lot of snags along the > > way (mostly in my time to get the code up to par for official inclusion). > > > > -Justin > > > > -- > > == > > > > Justin A. Lemkul, Ph.D. > > Assistant Professor > > Office: 301 Fralin Hall > > Lab: 303 Engel Hall > > > > Virginia Tech Department of Biochemistry > > 340 West Campus Dr. > > Blacksburg, VA 24061 > > > > jalem...@vt.edu | (540) 231-3129 > > http://www.thelemkullab.com > > > > == > > > > -- > > 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. > -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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] Drude force field
I've got the following Error. It seems this version of Gromacs does not recognize the Drude force field format distributed by MacKerell. There are additional Terms like [anisotropic_polarization] , etc.. Gromacs read this as a residue name. Program gmx, VERSION 5.0.7 Source code file: /data/cluster/apps/gromacs/source/gromacs-5.0.7/src/gromacs/gmxpreprocess/resall.c, line: 488 Fatal error: in .rtp file in residue anisotropic_polarization at line: DBR6 BR6C6C1C5 1.8000 0.6000 0.6000 On Thu, Jul 18, 2019 at 9:43 AM Justin Lemkul wrote: > > > On 7/17/19 8:39 PM, Myunggi Yi wrote: > > Dear users, > > > > I want to run a simulation with a polarizable force field. > > > > How and where can I get Drude force field for the current version of > > Gromacs? > > Everything you need to know: > > http://mackerell.umaryland.edu/charmm_drude_ff.shtml > > The implementation is not complete. If your system has ions, do not use > GROMACS due to the lack of NBTHOLE. In that case, use NAMD, CHARMM, or > OpenMM. The Drude model is still considered experimental, hence it is > not officially supported yet. There have been a lot of snags along the > way (mostly in my time to get the code up to par for official inclusion). > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > 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] Drude force field
Thank you Dr. Lemkel, I don't have ions in my simulation. It's a neutral system with a protein in membrane bilayer with solvent. I have downloaded the force field (Drude FF for charmm FF in Gromacs format). to run the simulation with charmm FF in "Gromacs 2019.3". However, it seems the format of the file does not match with the current version. In the web, Compile and install as you would any other (post-5.0) GROMACS version. If you attempt to use *ANY OTHER VERSION OF GROMACS, the Drude features will not be accessible.* There are 5.0 and 5.1 series of Gromacs versions. Which one should I use? Or, it there a way to modify the force field format to use the current version of Gromacs?, Then I will modify the format. On Thu, Jul 18, 2019 at 9:43 AM Justin Lemkul wrote: > > > On 7/17/19 8:39 PM, Myunggi Yi wrote: > > Dear users, > > > > I want to run a simulation with a polarizable force field. > > > > How and where can I get Drude force field for the current version of > > Gromacs? > > Everything you need to know: > > http://mackerell.umaryland.edu/charmm_drude_ff.shtml > > The implementation is not complete. If your system has ions, do not use > GROMACS due to the lack of NBTHOLE. In that case, use NAMD, CHARMM, or > OpenMM. The Drude model is still considered experimental, hence it is > not officially supported yet. There have been a lot of snags along the > way (mostly in my time to get the code up to par for official inclusion). > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > 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] Drude force field
Thank you. On Thu, Jul 18, 2019 at 9:43 AM Justin Lemkul wrote: > > > On 7/17/19 8:39 PM, Myunggi Yi wrote: > > Dear users, > > > > I want to run a simulation with a polarizable force field. > > > > How and where can I get Drude force field for the current version of > > Gromacs? > > Everything you need to know: > > http://mackerell.umaryland.edu/charmm_drude_ff.shtml > > The implementation is not complete. If your system has ions, do not use > GROMACS due to the lack of NBTHOLE. In that case, use NAMD, CHARMM, or > OpenMM. The Drude model is still considered experimental, hence it is > not officially supported yet. There have been a lot of snags along the > way (mostly in my time to get the code up to par for official inclusion). > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > 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] Drude force field
On 7/17/19 8:39 PM, Myunggi Yi wrote: Dear users, I want to run a simulation with a polarizable force field. How and where can I get Drude force field for the current version of Gromacs? Everything you need to know: http://mackerell.umaryland.edu/charmm_drude_ff.shtml The implementation is not complete. If your system has ions, do not use GROMACS due to the lack of NBTHOLE. In that case, use NAMD, CHARMM, or OpenMM. The Drude model is still considered experimental, hence it is not officially supported yet. There have been a lot of snags along the way (mostly in my time to get the code up to par for official inclusion). -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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] Drude force field
Dear users, I want to run a simulation with a polarizable force field. How and where can I get Drude force field for the current version of Gromacs? Thank you. -- 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] Drude force field
Dear users, How or where can I get the Drude polarizable force field file for current Gromacs version? -- 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] Drude force field
On 7/20/17 8:08 AM, Shraddha Parate wrote: Hi gmx users! For polarizable effect, I was setting drude force field in Gromacs I attempted running Lagrangian Dynamics simulation using Drude force field. mdp file format was used from the supporting data in below paper. [2015] Implementation of extended Lagrangian dynamics in GROMACS for polarizable simulations using the classical Drude oscillator model.( http://onlinelibrary.wiley.com/doi/10.1002/jcc.23937/abstract;jsessionid=E354008D7BE6AA1A02D26C061B49163A.f02t01 ) --- ; RUN CONTROL PARAMETERS integrator = md-vv ; Start time and timestep in ps tinit = 0 dt = 0.001 nsteps = 1 comm-mode = linear nstcomm = 100 comm-grps = System ; OUTPUT CONTROL OPTIONS nstxout = 1000 nstvout = 1000 nstfout = 1000 ; Output frequency for energies to log file and energy file nstlog = 100 nstcalcenergy = 100 nstenergy = 100 ; NEIGHBORSEARCHING PARAMETERS cutoff-scheme = verlet nstlist = 10 ns-type = Grid pbc = xyz rlist = 1.2 ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype = PME rcoulomb = 1.2 vdwtype = cutoff vdw-modifier = potential-switch rvdw-switch = 1.0 rvdw = 1.2 DispCorr = EnerPres ; TEMPERATURE COUPLING tcoupl = Nose-Hoover nsttcouple = 1 nh-chain-length = 1 ; Groups to couple separately tc-grps = Atoms Drues tau-t = 0.1 0.005 ref-t = 298.15 1.0 ; GENERATE VELOCITIES FOR STARTUP RUN, OTHERWISE DO ; NOT GENERATE NEW VELOCITIES IF PREVIOUSLY EQUILIBRATED gen-vel = yes gen-temp = 298.15 gen-seed = -1 ; OPTIONS FOR BONDS constraints = none ; can also be h-bonds, not all-bonds continuation = no ; DRUDE PARAMETERS drude = yes drude-mode = Lagrangian drude-t = 1.0 drude-hardwall = yes drude-r = 0.02 drude-tsteps = 5 --- I couldn't understand [tc-grps = Atoms Drude] option. All the atoms in one group, all the Drudes in the next. If you want to break the system apart into protein and non-protein: tc-grps = Protein-Atoms Protein Drudes Non-Protein-Atoms Non-Protein-Drudes ref_t = 298.15 1.0 298.15 1.0 tau_t = 1.0 0.005 1.0 0.005 If the option is changed to [tc-grps = Protein SOL],I get a fatal error message. -- Fatal error: Incorrect thermostat setup in relative_tstat, ti = -1 -- How to resolve this issue? Why the changed parameter gives a fatal error? Do what the paper (and the ones cited therein) tell you to do. The Drude integration scheme requires a special dual thermostat that couples the Drude oscillators to a low-temperature thermostat to approximate the SCF surface. You can't treat these kinds of systems like you would additive ones. The atoms (anything non-Drude) and Drudes have to be in separate thermostats, in a given order, as explained in the paper (and shown above). Note that domain decomposition remains broken, so you can only run with OpenMP. I recently identified the (hopefully) last remaining issue but it will take some time to get it fixed as I am currently moving and starting my own lab, so my attention is elsewhere for a while. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 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] Drude force field
Hi gmx users! For polarizable effect, I was setting drude force field in Gromacs I attempted running Lagrangian Dynamics simulation using Drude force field. mdp file format was used from the supporting data in below paper. [2015] Implementation of extended Lagrangian dynamics in GROMACS for polarizable simulations using the classical Drude oscillator model.( http://onlinelibrary.wiley.com/doi/10.1002/jcc.23937/abstract;jsessionid=E354008D7BE6AA1A02D26C061B49163A.f02t01 ) --- ; RUN CONTROL PARAMETERS integrator = md-vv ; Start time and timestep in ps tinit = 0 dt = 0.001 nsteps = 1 comm-mode = linear nstcomm = 100 comm-grps = System ; OUTPUT CONTROL OPTIONS nstxout = 1000 nstvout = 1000 nstfout = 1000 ; Output frequency for energies to log file and energy file nstlog = 100 nstcalcenergy = 100 nstenergy = 100 ; NEIGHBORSEARCHING PARAMETERS cutoff-scheme = verlet nstlist = 10 ns-type = Grid pbc = xyz rlist = 1.2 ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype = PME rcoulomb = 1.2 vdwtype = cutoff vdw-modifier = potential-switch rvdw-switch = 1.0 rvdw = 1.2 DispCorr = EnerPres ; TEMPERATURE COUPLING tcoupl = Nose-Hoover nsttcouple = 1 nh-chain-length = 1 ; Groups to couple separately tc-grps = Atoms Drues tau-t = 0.1 0.005 ref-t = 298.15 1.0 ; GENERATE VELOCITIES FOR STARTUP RUN, OTHERWISE DO ; NOT GENERATE NEW VELOCITIES IF PREVIOUSLY EQUILIBRATED gen-vel = yes gen-temp = 298.15 gen-seed = -1 ; OPTIONS FOR BONDS constraints = none ; can also be h-bonds, not all-bonds continuation = no ; DRUDE PARAMETERS drude = yes drude-mode = Lagrangian drude-t = 1.0 drude-hardwall = yes drude-r = 0.02 drude-tsteps = 5 --- I couldn't understand [tc-grps = Atoms Drude] option. If the option is changed to [tc-grps = Protein SOL],I get a fatal error message. -- Fatal error: Incorrect thermostat setup in relative_tstat, ti = -1 -- How to resolve this issue? Why the changed parameter gives a fatal error? I look forward to your response. Thank you for reading. -- 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] Drude force field
On 10/28/16 3:27 PM, Xianchi Dong wrote: I simply put the ff files to the working folder and used the previous installed Gromacs 5.1.2. When use pdb2gmx, it gives the error msg: Fatal error: in .rtp file in residue anisotropic_polarization at line: DO1O1C1 LP1A LP1B 0.8108 1.2162 0.9730 Could you give me some advise? The Drude features are in the "drude" development branch only. You cannot use released GROMACS versions. See the instructions on the linked page I posted earlier. -Justin Best, Xianchi On Fri, Oct 28, 2016 at 3:17 PM, Justin Lemkul wrote: On 10/28/16 2:48 PM, Xianchi Dong wrote: Thanks for your reply. Do I need to copy the ff file to any folder? Either the working directory or $GMXLIB, like any other force field. -Justin Best, Xianchi On Oct 28, 2016, at 1:56 PM, Justin Lemkul wrote: On 10/28/16 1:39 PM, Xianchi Dong wrote: Dear all, Does anyone have a detailed protocol to install Drude polarized force field on Gromacs? There's nothing special about installation or use: http://mackerell.umaryland.edu/charmm_drude_ff.shtml Be aware that runs using domain decomposition may crash due to an as-yet unresolved bug. I'm working on it, but it's below certain other priorities at the moment. OpenMP runs are fine. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 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 629 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 629 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] Drude force field
I simply put the ff files to the working folder and used the previous installed Gromacs 5.1.2. When use pdb2gmx, it gives the error msg: Fatal error: in .rtp file in residue anisotropic_polarization at line: DO1O1C1 LP1A LP1B 0.8108 1.2162 0.9730 Could you give me some advise? Best, Xianchi On Fri, Oct 28, 2016 at 3:17 PM, Justin Lemkul wrote: > > > On 10/28/16 2:48 PM, Xianchi Dong wrote: > >> Thanks for your reply. >> Do I need to copy the ff file to any folder? >> >> > Either the working directory or $GMXLIB, like any other force field. > > -Justin > > > Best, >> Xianchi >> >> On Oct 28, 2016, at 1:56 PM, Justin Lemkul wrote: >>> >>> >>> >>> On 10/28/16 1:39 PM, Xianchi Dong wrote: Dear all, Does anyone have a detailed protocol to install Drude polarized force field on Gromacs? >>> There's nothing special about installation or use: >>> >>> http://mackerell.umaryland.edu/charmm_drude_ff.shtml >>> >>> Be aware that runs using domain decomposition may crash due to an as-yet >>> unresolved bug. I'm working on it, but it's below certain other priorities >>> at the moment. OpenMP runs are fine. >>> >>> -Justin >>> >>> -- >>> == >>> >>> Justin A. Lemkul, Ph.D. >>> Ruth L. Kirschstein NRSA Postdoctoral Fellow >>> >>> Department of Pharmaceutical Sciences >>> School of Pharmacy >>> Health Sciences Facility II, Room 629 >>> 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 629 > 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] Drude force field
On 10/28/16 2:48 PM, Xianchi Dong wrote: Thanks for your reply. Do I need to copy the ff file to any folder? Either the working directory or $GMXLIB, like any other force field. -Justin Best, Xianchi On Oct 28, 2016, at 1:56 PM, Justin Lemkul wrote: On 10/28/16 1:39 PM, Xianchi Dong wrote: Dear all, Does anyone have a detailed protocol to install Drude polarized force field on Gromacs? There's nothing special about installation or use: http://mackerell.umaryland.edu/charmm_drude_ff.shtml Be aware that runs using domain decomposition may crash due to an as-yet unresolved bug. I'm working on it, but it's below certain other priorities at the moment. OpenMP runs are fine. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 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 629 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] Drude force field
Thanks for your reply. Do I need to copy the ff file to any folder? Best, Xianchi > On Oct 28, 2016, at 1:56 PM, Justin Lemkul wrote: > > > >> On 10/28/16 1:39 PM, Xianchi Dong wrote: >> Dear all, >> Does anyone have a detailed protocol to install Drude polarized force field >> on Gromacs? >> > > There's nothing special about installation or use: > > http://mackerell.umaryland.edu/charmm_drude_ff.shtml > > Be aware that runs using domain decomposition may crash due to an as-yet > unresolved bug. I'm working on it, but it's below certain other priorities > at the moment. OpenMP runs are fine. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > 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] Drude force field
On 10/28/16 1:39 PM, Xianchi Dong wrote: Dear all, Does anyone have a detailed protocol to install Drude polarized force field on Gromacs? There's nothing special about installation or use: http://mackerell.umaryland.edu/charmm_drude_ff.shtml Be aware that runs using domain decomposition may crash due to an as-yet unresolved bug. I'm working on it, but it's below certain other priorities at the moment. OpenMP runs are fine. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 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] Drude force field
Dear all, Does anyone have a detailed protocol to install Drude polarized force field on Gromacs? Best, Xianchi -- 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.