RE: [gmx-users] about NPT run
Hi, For position restraints there is an mdp option refcoord_scaling that sets how the reference positions are affected by pressure scaling. Berk Date: Thu, 16 Sep 2010 21:15:38 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] about NPT run zhongjin wrote: Hi, I want to run a NPT run,could I put some groups into position restraint, or make them frozened ? I find it is OK in NVT ensemble. But I am not sure whether it is proper. Frozen groups cannot have their coordinates scaled by pressure coupling. I believe this can lead to spurious contributions to the virial and pressure, so it is generally recommended that NPT not be combined with frozen groups. -Justin Thanks! Zhongjin He -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] ARG Charmm gmx 4.5.1
Dear Gromacs Users, I am using plain cutoff for my 12-mer protein. The grompp reports ARG to have a big charge group. this was also highlighted in the following mail http://www.mail-archive.com/gmx-users@gromacs.org/msg32098.html I was just think if changing the charges on these atoms would help, from 13 CT2 1 ARG CD 4 0.2 12.011 ; qtot 1.2 14 HA 1 ARG HD1 4 0.09 1.008 ; qtot 1.29 15 HA 1 ARG HD2 4 0.09 1.008 ; qtot 1.38 16 NC2 1 ARG NE 4 -0.7 14.007 ; qtot 0.68 17 HC 1 ARG HE 4 0.44 1.008 ; qtot 1.12 18 C 1 ARG CZ 4 0.64 12.011 ; qtot 1.76 19 NC2 1 ARG NH1 4 -0.8 14.007 ; qtot 0.96 20 HC 1 ARG HH11 4 0.46 1.008 ; qtot 1.42 21 HC 1 ARG HH12 4 0.46 1.008 ; qtot 1.88 22 NC2 1 ARG NH2 4 -0.8 14.007 ; qtot 1.08 23 HC 1 ARG HH21 4 0.46 1.008 ; qtot 1.54 24 HC 1 ARG HH22 4 0.46 1.008 ; qtot 2 to CD 0.18 HD1 0.06 HD2 0.06 NE -0.7 HE 0.4 CZ 0.6 NH1 -0.8 HH11 0.5 HH12 0.5 NH2 -0.8 HH21 0.5 HH22 0.5 The above transformation of charges seems reasonable. Would like to know if this is okay... Best, nahren -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] ARG Charmm gmx 4.5.1
Hi, No, you should never change the charges in a force field! Run pdb2gmx again with the -nochargegrp option. That will make the size of all charge groups a single atom. This will be done automatically in the 4.5.2 release which will be out soon. Berk Date: Fri, 17 Sep 2010 02:32:31 -0700 From: meetnah...@yahoo.com To: gmx-users@gromacs.org Subject: [gmx-users] ARG Charmm gmx 4.5.1 Dear Gromacs Users, I am using plain cutoff for my 12-mer protein. The grompp reports ARG to have a big charge group. this was also highlighted in the following mail http://www.mail-archive.com/gmx-users@gromacs.org/msg32098.html I was just think if changing the charges on these atoms would help, from 13CT2 1ARG CD 40.2 12.011 ; qtot 1.2 14 HA 1ARGHD1 4 0.09 1.008 ; qtot 1.29 15 HA 1ARGHD2 4 0.09 1.008 ; qtot 1.38 16NC2 1ARG NE 4 -0.7 14.007 ; qtot 0.68 17 HC 1ARG HE 4 0.44 1.008 ; qtot 1.12 18 C 1ARG CZ 4 0.64 12.011 ; qtot 1.76 19NC2 1 ARGNH1 4 -0.8 14.007 ; qtot 0.96 20 HC 1ARG HH11 4 0.46 1.008 ; qtot 1.42 21 HC 1ARG HH12 4 0.46 1.008 ; qtot 1.88 22NC2 1ARGNH2 4 -0.8 14.007 ; qtot 1.08 23 HC 1ARG HH21 4 0.46 1.008 ; qtot 1.54 24 HC 1ARG HH22 4 0.46 1.008 ; qtot 2 to Message body CD0.18 HD10.06 HD20.06 NE-0.7 HE0.4 CZ0.6 NH1-0.8 HH110.5 HH120.5 NH2-0.8 HH210.5 HH220.5 The above transformation of charges seems reasonable. Would like to know if this is okay... Best, nahren -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] ARG Charmm gmx 4.5.1
You should change the charge group number. Every charge group include several, like 3-4, atoms. Actually, the definition of charge group is not significant if you use PME for the coulomb interaction. nahren manuel wrote: Dear Gromacs Users, I am using plain cutoff for my 12-mer protein. The grompp reports ARG to have a big charge group. this was also highlighted in the following mail http://www.mail-archive.com/gmx-users@gromacs.org/msg32098.html I was just think if changing the charges on these atoms would help, from 13CT2 1ARG CD 40.2 12.011 ; qtot 1.2 14 HA 1ARGHD1 4 0.09 1.008 ; qtot 1.29 15 HA 1ARGHD2 4 0.09 1.008 ; qtot 1.38 16NC2 1ARG NE 4 -0.7 14.007 ; qtot 0.68 17 HC 1ARG HE 4 0.44 1.008 ; qtot 1.12 18 C 1ARG CZ 4 0.64 12.011 ; qtot 1.76 19NC2 1ARGNH1 4 -0.8 14.007 ; qtot 0.96 20 HC 1ARG HH11 4 0.46 1.008 ; qtot 1.42 21 HC 1ARG HH12 4 0.46 1.008 ; qtot 1.88 22NC2 1ARGNH2 4 -0.8 14.007 ; qtot 1.08 23 HC 1ARG HH21 4 0.46 1.008 ; qtot 1.54 24 HC 1ARG HH22 4 0.46 1.008 ; qtot 2 to CD0.18 HD10.06 HD20.06 NE-0.7 HE0.4 CZ0.6 NH1-0.8 HH110.5 HH120.5 NH2-0.8 HH210.5 HH220.5 The above transformation of charges seems reasonable. Would like to know if this is okay... Best, nahren -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] ARG Charmm gmx 4.5.1
Hi, The choice of charge is significant even with PME, because of the way Gromacs makes the neighborlists. As I mailed before, use the -nochargegrp option of pdb2gmx with the Charmm27 ff. Berk Date: Fri, 17 Sep 2010 11:46:36 +0200 From: qia...@gmail.com To: gmx-users@gromacs.org Subject: Re: [gmx-users] ARG Charmm gmx 4.5.1 You should change the charge group number. Every charge group include several, like 3-4, atoms. Actually, the definition of charge group is not significant if you use PME for the coulomb interaction. nahren manuel wrote: Dear Gromacs Users, I am using plain cutoff for my 12-mer protein. The grompp reports ARG to have a big charge group. this was also highlighted in the following mail http://www.mail-archive.com/gmx-users@gromacs.org/msg32098.html I was just think if changing the charges on these atoms would help, from 13CT2 1ARG CD 40.2 12.011 ; qtot 1.2 14 HA 1ARGHD1 4 0.09 1.008 ; qtot 1.29 15 HA 1ARGHD2 4 0.09 1.008 ; qtot 1.38 16NC2 1ARG NE 4 -0.7 14.007 ; qtot 0.68 17 HC 1ARG HE 4 0.44 1.008 ; qtot 1.12 18 C 1ARG CZ 4 0.64 12.011 ; qtot 1.76 19NC2 1ARGNH1 4 -0.8 14.007 ; qtot 0.96 20 HC 1ARG HH11 4 0.46 1.008 ; qtot 1.42 21 HC 1ARG HH12 4 0.46 1.008 ; qtot 1.88 22NC2 1ARGNH2 4 -0.8 14.007 ; qtot 1.08 23 HC 1ARG HH21 4 0.46 1.008 ; qtot 1.54 24 HC 1ARG HH22 4 0.46 1.008 ; qtot 2 to CD0.18 HD10.06 HD20.06 NE-0.7 HE0.4 CZ0.6 NH1-0.8 HH110.5 HH120.5 NH2-0.8 HH210.5 HH220.5 The above transformation of charges seems reasonable. Would like to know if this is okay... Best, nahren -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Nucleotides for charmm port
Hi all, Has anybody managed to use ATP with the charmm27 ff in gromacs 4.5? The forcefield files are missing atom and bond types and angle information. This is available for charmm, but I have only found it in stream file and have no idea how to convert it. It should be possible (for someone smarter than me). cheers Dave -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] WHAM
Anirban Ghosh wrote: Hi Justin, Thanks a lot for the reply. Yes I have had a look at section 4.4.2. But section 5.3 tells that this WHAM can be used with the REMD data set as well. So my question is that how to present this REMD data of multiple trajectories as input to WHAM? Do I need to work around with the WHAM code or there is some other way? Also in section 5.3 is the procedure for how to use REMD data, but I don't think it will ever accomplish what you want. The input into WHAM would be energies, not RMSD vs. R(g), as you initially stated as your goal. You can easily build free energy surfaces of RMSD vs. R(g) using g_sham, however. -Justin Any suggestion is welcome. Thanks again. Regards, Anirban On Thu, Sep 16, 2010 at 5:28 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Anirban Ghosh wrote: Hi ALL, I have carried out REMD simulation on a protein (20 replicas). Now I want to carry 2D PMF calculation using RMSD and Radius of gyration as the reaction coordinates using Grossfield Lab's WHAM package. For this what should be my input parameters to the WHAM program and in which format? Any suggestion in this regard is welcome. I would suggest you consult the documentation for the program (i.e. the Grossfield WHAM manual, section 4.2.2). I don't know how you intend to pass your data to a program that is designed for umbrella sampling, but I suppose that's your task. -Justin Regards, Anirban -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Nucleotides for charmm port
Have you looked in the ffnabonded.itp and ffnanonbonded.itp? To me it looks like all of the atom types/bonds/angles are there. I have just made a very quick rtp entry from the stream file (see attached) and it seems to work fine (but please do check it). Note the very large charge groups, so you should use the -nochargegrp option of pdb2gmx. Cheers Tom David Parcej wrote: Hi all, Has anybody managed to use ATP with the charmm27 ff in gromacs 4.5? The forcefield files are missing atom and bond types and angle information. This is available for charmm, but I have only found it in stream file and have no idea how to convert it. It should be possible (for someone smarter than me). cheers Dave -- Dr Thomas Piggot University of Southampton, UK. [ bondedtypes ] ; Col 1: Type of bond ; Col 2: Type of angles ; Col 3: Type of proper dihedrals ; Col 4: Type of improper dihedrals ; Col 5: Generate all dihedrals if 1, only heavy atoms of 0. ; Col 6: Number of excluded neighbors for nonbonded interactions ; Col 7: Generate 1,4 interactions between pairs of hydrogens if 1 ; Col 8: Remove propers over the same bond as an improper if it is 1 ; bonds angles dihedrals impropers all_dihedrals nrexcl HH14 RemoveDih 1 5 921 3 1 0 [ATP] ; ; from toppar_all27_na_nad_ppi.str. Thomas Piggot 17/9/10 ; [atoms] C4' CN7 0.16 0 H4' HN7 0.09 0 O4' ON6B -0.50 0 C1' CN7B0.16 0 H1' HN7 0.09 0 C5 CN5 0.28 1 N7 NN4-0.71 1 C8 CN4 0.34 1 H8 HN3 0.12 1 N9 NN2-0.05 1 N1 NN3A -0.74 2 C2 CN4 0.50 2 H2 HN3 0.13 2 N3 NN3A -0.75 2 C4 CN5 0.43 2 C6 CN2 0.46 2 N6 NN1-0.77 3 H61 HN1 0.38 3 H62 HN1 0.38 3 C2' CN7B0.14 4 H2'' HN7 0.09 4 O2' ON5-0.66 4 H2' HN5 0.43 4 C3' CN7 0.14 5 H3' HN7 0.09 5 O3' ON5-0.66 5 H3T HN5 0.43 5 C5' CN8B -0.08 6 H5' HN8 0.09 6 H5'' HN8 0.09 6 O5' ON2-0.62 6 PA P 1.50 6 O1A ON3-0.82 6 O2A ON3-0.82 6 O3A ON2-0.74 6 PB P2 1.50 6 O1B ON3-0.82 6 O2B ON3-0.82 6 O3B ON2-0.86 6 PG P2 1.10 6 O1G ON3-0.90 6 O2G ON3-0.90 6 O3G ON3-0.90 6 [bonds] O5' C5' O5' PA PA O1A PA O2A PA O3A O3A PB PB O1B PB O2B PB O3B O3B PG PG O1G PG O2G PG O3G C5' C4' C4' O4' C4' C3' O4' C1' C1' N9 C1' C2' N9 C4 N9 C8 C4 N3 C2 N1 C6 N6 N6 H61 N6 H62 C6 C5 C5 N7 C2' C3' C2' O2' O2' H2' C3' O3' O3' H3T C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' C5' H5'' C8 H8 C2 H2 N1 C6 N3 C2 C4 C5 N7 C8 [impropers] N6 C6 H61 H62 C6 N1 C5 N6 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] ARG Charmm gmx 4.5.1
Hi Berk and others, I have been wondering if there was another way to treat the large charge groups for the CHARMM forcefield(s) in GROMACS, rather than using the -nochargegrp option. The reason I ask is because changing every atom to be in individual charge groups changes the forcefield (albeit slightly) from its original implementation and it would be good to be able to use the forcefields in as close a way as possible as to how they were originally used in CHARMM. I suppose another way to do it is to increase the cutoff's, however changing the cutoff's from their original intended values is also undesirable and this can also significantly impact on performance. Whether this is better or worse (in the sense of the difference to how the forcefields were originally used in CHARMM) than using -nochargegrp I am not sure. I also noticed that in version 4.5 there is a rlistlong parameter, could this be used to account for the large charge groups rather than increasing other cutoff's? Can anyone think of any other ways to do this? I have no idea if it be easy/possible to implement an option to use the CHARMM approach for treating charge groups (as I understand it when any atom is within the cutoff then the whole charge group is included). Sorry for the fairly long message and thanks for any insights you can give. Tom Berk Hess wrote: Hi, No, you should never change the charges in a force field! Run pdb2gmx again with the -nochargegrp option. That will make the size of all charge groups a single atom. This will be done automatically in the 4.5.2 release which will be out soon. Berk Date: Fri, 17 Sep 2010 02:32:31 -0700 From: meetnah...@yahoo.com To: gmx-users@gromacs.org Subject: [gmx-users] ARG Charmm gmx 4.5.1 Dear Gromacs Users, I am using plain cutoff for my 12-mer protein. The grompp reports ARG to have a big charge group. this was also highlighted in the following mail http://www.mail-archive.com/gmx-users@gromacs.org/msg32098.html I was just think if changing the charges on these atoms would help, from 13CT2 1ARG CD 40.2 12.011 ; qtot 1.2 14 HA 1ARGHD1 4 0.09 1.008 ; qtot 1.29 15 HA 1ARGHD2 4 0.09 1.008 ; qtot 1.38 16NC2 1ARG NE 4 -0.7 14.007 ; qtot 0.68 17 HC 1ARG HE 4 0.44 1.008 ; qtot 1.12 18 C 1ARG CZ 4 0.64 12.011 ; qtot 1.76 19NC2 1ARGNH1 4 -0.8 14.007 ; qtot 0.96 20 HC 1ARG HH11 4 0.46 1.008 ; qtot 1.42 21 HC 1ARG HH12 4 0.46 1.008 ; qtot 1.88 22NC2 1ARGNH2 4 -0.8 14.007 ; qtot 1.08 23 HC 1ARG HH21 4 0.46 1.008 ; qtot 1.54 24 HC 1ARG HH22 4 0.46 1.008 ; qtot 2 to CD0.18 HD10.06 HD20.06 NE-0.7 HE0.4 CZ0.6 NH1-0.8 HH110.5 HH120.5 NH2-0.8 HH210.5 HH220.5 The above transformation of charges seems reasonable. Would like to know if this is okay... Best, nahren -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] ARG Charmm gmx 4.5.1
Hi, I think there is no point in exactly copying the way a certain program treats things technically, except for checking force field implementation, but since that can be done without cut-off's there no real need. Charge groups are an ancient leftover from the old times when plain cut-off's were used. I don't actually know if Charmm uses charge groups with PME. But having no charge-groups at all leads to no artifacts, so that's the best solution anyhow. I will try to completely get rid of charge groups in Gromacs in the next major release, so we get rid of these issues once and for all. Berk Date: Fri, 17 Sep 2010 14:12:51 +0100 From: t.pig...@soton.ac.uk To: gmx-users@gromacs.org Subject: Re: [gmx-users] ARG Charmm gmx 4.5.1 Hi Berk and others, I have been wondering if there was another way to treat the large charge groups for the CHARMM forcefield(s) in GROMACS, rather than using the -nochargegrp option. The reason I ask is because changing every atom to be in individual charge groups changes the forcefield (albeit slightly) from its original implementation and it would be good to be able to use the forcefields in as close a way as possible as to how they were originally used in CHARMM. I suppose another way to do it is to increase the cutoff's, however changing the cutoff's from their original intended values is also undesirable and this can also significantly impact on performance. Whether this is better or worse (in the sense of the difference to how the forcefields were originally used in CHARMM) than using -nochargegrp I am not sure. I also noticed that in version 4.5 there is a rlistlong parameter, could this be used to account for the large charge groups rather than increasing other cutoff's? Can anyone think of any other ways to do this? I have no idea if it be easy/possible to implement an option to use the CHARMM approach for treating charge groups (as I understand it when any atom is within the cutoff then the whole charge group is included). Sorry for the fairly long message and thanks for any insights you can give. Tom Berk Hess wrote: Hi, No, you should never change the charges in a force field! Run pdb2gmx again with the -nochargegrp option. That will make the size of all charge groups a single atom. This will be done automatically in the 4.5.2 release which will be out soon. Berk Date: Fri, 17 Sep 2010 02:32:31 -0700 From: meetnah...@yahoo.com To: gmx-users@gromacs.org Subject: [gmx-users] ARG Charmm gmx 4.5.1 Dear Gromacs Users, I am using plain cutoff for my 12-mer protein. The grompp reports ARG to have a big charge group. this was also highlighted in the following mail http://www.mail-archive.com/gmx-users@gromacs.org/msg32098.html I was just think if changing the charges on these atoms would help, from 13CT2 1ARG CD 40.2 12.011 ; qtot 1.2 14 HA 1ARGHD1 4 0.09 1.008 ; qtot 1.29 15 HA 1ARGHD2 4 0.09 1.008 ; qtot 1.38 16NC2 1ARG NE 4 -0.7 14.007 ; qtot 0.68 17 HC 1ARG HE 4 0.44 1.008 ; qtot 1.12 18 C 1ARG CZ 4 0.64 12.011 ; qtot 1.76 19NC2 1ARGNH1 4 -0.8 14.007 ; qtot 0.96 20 HC 1ARG HH11 4 0.46 1.008 ; qtot 1.42 21 HC 1ARG HH12 4 0.46 1.008 ; qtot 1.88 22NC2 1ARGNH2 4 -0.8 14.007 ; qtot 1.08 23 HC 1ARG HH21 4 0.46 1.008 ; qtot 1.54 24 HC 1ARG HH22 4 0.46 1.008 ; qtot 2 to CD0.18 HD10.06 HD20.06 NE-0.7 HE0.4 CZ0.6 NH1-0.8 HH110.5 HH120.5 NH2-0.8 HH210.5 HH220.5 The above transformation of charges seems reasonable. Would like to know if this is okay... Best, nahren -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org.
RE: [gmx-users] ARG Charmm gmx 4.5.1
Hi, I just got a mail from a CHARMM developer saying that charge groups in CHARMM have no influence on the way forces are calculated. The details of the use of charge groups in CHARMM are not how I guessed they were, but the conclusion is that one should use no charge groups (or single atom charge groups to be more precise) for the CHARMM force field in Gromacs. Berk From: g...@hotmail.com To: gmx-users@gromacs.org Subject: RE: [gmx-users] ARG Charmm gmx 4.5.1 Date: Fri, 17 Sep 2010 15:46:56 +0200 Hi, I think there is no point in exactly copying the way a certain program treats things technically, except for checking force field implementation, but since that can be done without cut-off's there no real need. Charge groups are an ancient leftover from the old times when plain cut-off's were used. I don't actually know if Charmm uses charge groups with PME. But having no charge-groups at all leads to no artifacts, so that's the best solution anyhow. I will try to completely get rid of charge groups in Gromacs in the next major release, so we get rid of these issues once and for all. Berk Date: Fri, 17 Sep 2010 14:12:51 +0100 From: t.pig...@soton.ac.uk To: gmx-users@gromacs.org Subject: Re: [gmx-users] ARG Charmm gmx 4.5.1 Hi Berk and others, I have been wondering if there was another way to treat the large charge groups for the CHARMM forcefield(s) in GROMACS, rather than using the -nochargegrp option. The reason I ask is because changing every atom to be in individual charge groups changes the forcefield (albeit slightly) from its original implementation and it would be good to be able to use the forcefields in as close a way as possible as to how they were originally used in CHARMM. I suppose another way to do it is to increase the cutoff's, however changing the cutoff's from their original intended values is also undesirable and this can also significantly impact on performance. Whether this is better or worse (in the sense of the difference to how the forcefields were originally used in CHARMM) than using -nochargegrp I am not sure. I also noticed that in version 4.5 there is a rlistlong parameter, could this be used to account for the large charge groups rather than increasing other cutoff's? Can anyone think of any other ways to do this? I have no idea if it be easy/possible to implement an option to use the CHARMM approach for treating charge groups (as I understand it when any atom is within the cutoff then the whole charge group is included). Sorry for the fairly long message and thanks for any insights you can give. Tom Berk Hess wrote: Hi, No, you should never change the charges in a force field! Run pdb2gmx again with the -nochargegrp option. That will make the size of all charge groups a single atom. This will be done automatically in the 4.5.2 release which will be out soon. Berk Date: Fri, 17 Sep 2010 02:32:31 -0700 From: meetnah...@yahoo.com To: gmx-users@gromacs.org Subject: [gmx-users] ARG Charmm gmx 4.5.1 Dear Gromacs Users, I am using plain cutoff for my 12-mer protein. The grompp reports ARG to have a big charge group. this was also highlighted in the following mail http://www.mail-archive.com/gmx-users@gromacs.org/msg32098.html I was just think if changing the charges on these atoms would help, from 13CT2 1ARG CD 40.2 12.011 ; qtot 1.2 14 HA 1ARGHD1 4 0.09 1.008 ; qtot 1.29 15 HA 1ARGHD2 4 0.09 1.008 ; qtot 1.38 16NC2 1ARG NE 4 -0.7 14.007 ; qtot 0.68 17 HC 1ARG HE 4 0.44 1.008 ; qtot 1.12 18 C 1ARG CZ 4 0.64 12.011 ; qtot 1.76 19NC2 1ARGNH1 4 -0.8 14.007 ; qtot 0.96 20 HC 1ARG HH11 4 0.46 1.008 ; qtot 1.42 21 HC 1ARG HH12 4 0.46 1.008 ; qtot 1.88 22NC2 1ARGNH2 4 -0.8 14.007 ; qtot 1.08 23 HC 1ARG HH21 4 0.46 1.008 ; qtot 1.54 24 HC 1ARG HH22 4 0.46 1.008 ; qtot 2 to CD0.18 HD10.06 HD20.06 NE-0.7 HE0.4 CZ0.6 NH1-0.8 HH110.5 HH120.5 NH2-0.8 HH210.5 HH220.5 The above transformation of charges seems reasonable. Would like to know if this is okay... Best, nahren -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the
[gmx-users] Re:problem adding H atoms
Hi Justin, the gromacs version is 4.0.4. command line: pdb2gmx -f 1B9Eostate.pdb -o 1B9Eostate.gro -p 1B9Eostate.top -ff amber03 message: WARNING: atom H is missing in residue ILE 2 in the pdb file You might need to add atom H to the hydrogen database of residue ILE in the file ff???.hdb (see the manual) beginning of pdb file: ATOM 1 N NGLYA 1 -5.201 9.673 -2.852 1.00 21.99 N ATOM 2 CA NGLYA 1 -3.724 9.368 -2.711 1.00 21.30 C ATOM 3 C NGLYA 1 -3.320 8.030 -3.324 1.00 18.48 C ATOM 4 O NGLYA 1 -4.164 7.323 -3.878 1.00 24.81 O ATOM 5 N ILE A 2 -2.065 7.644 -3.159 1.00 13.65 N ATOM 6 CA ILE A 2 -1.579 6.399 -3.716 1.00 12.18 C ATOM 7 C ILE A 2 -2.254 5.174 -3.077 1.00 15.61 C ATOM 8 O ILE A 2 -2.629 4.249 -3.786 1.00 13.09 O ATOM 9 CB ILE A 2 -0.037 6.325 -3.601 1.00 12.48 C ATOM 10 CG1 ILE A 2 0.494 5.122 -4.357 1.00 14.27 C ATOM 11 CG2 ILE A 2 0.397 6.250 -2.171 1.00 7.71 C ATOM 12 CD ILE A 2 1.946 5.193 -4.618 1.00 11.64 C ATOM 13 N VAL A 3 -2.487 5.202 -1.759 1.00 19.67 N ATOM 14 CA VAL A 3 -3.123 4.072 -1.065 1.00 21.16 C ATOM 15 C VAL A 3 -4.531 3.814 -1.605 1.00 21.76 C ATOM 16 O VAL A 3 -4.954 2.670 -1.806 1.00 20.69 O ATOM 17 CB VAL A 3 -3.225 4.312 0.465 1.00 21.43 C ATOM 18 CG1 VAL A 3 -3.687 3.033 1.165 1.00 21.34 C ATOM 19 CG2 VAL A 3 -1.885 4.782 1.039 1.00 19.65 C -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] potential energy in implicit solvent simulations
Hi It seems that the non-polar energy term has gone missing, and does not get included in the print-out. While adding it back again properly I found some other issues that I need to check before committing. The total potential energy should be correct. /Per 16 sep 2010 kl. 17:47 skrev Ehud Schreiber schr...@compugen.co.il: Can you explain this situation? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re:problem adding H atoms
Stacey Meadley wrote: Hi Justin, the gromacs version is 4.0.4. command line: pdb2gmx -f 1B9Eostate.pdb -o 1B9Eostate.gro -p 1B9Eostate.top -ff amber03 message: WARNING: atom H is missing in residue ILE 2 in the pdb file You might need to add atom H to the hydrogen database of residue ILE in the file ff???.hdb (see the manual) beginning of pdb file: ATOM 1 N NGLYA 1 -5.201 9.673 -2.852 1.00 21.99 N ATOM 2 CA NGLYA 1 -3.724 9.368 -2.711 1.00 21.30 C ATOM 3 C NGLYA 1 -3.320 8.030 -3.324 1.00 18.48 C ATOM 4 O NGLYA 1 -4.164 7.323 -3.878 1.00 24.81 O ATOM 5 N ILE A 2 -2.065 7.644 -3.159 1.00 13.65 N ATOM 6 CA ILE A 2 -1.579 6.399 -3.716 1.00 12.18 C ATOM 7 C ILE A 2 -2.254 5.174 -3.077 1.00 15.61 C ATOM 8 O ILE A 2 -2.629 4.249 -3.786 1.00 13.09 O ATOM 9 CB ILE A 2 -0.037 6.325 -3.601 1.00 12.48 C ATOM 10 CG1 ILE A 2 0.494 5.122 -4.357 1.00 14.27 C ATOM 11 CG2 ILE A 2 0.397 6.250 -2.171 1.00 7.71 C ATOM 12 CD ILE A 2 1.946 5.193 -4.618 1.00 11.64 C ATOM 13 N VAL A 3 -2.487 5.202 -1.759 1.00 19.67 N ATOM 14 CA VAL A 3 -3.123 4.072 -1.065 1.00 21.16 C ATOM 15 C VAL A 3 -4.531 3.814 -1.605 1.00 21.76 C ATOM 16 O VAL A 3 -4.954 2.670 -1.806 1.00 20.69 O ATOM 17 CB VAL A 3 -3.225 4.312 0.465 1.00 21.43 C ATOM 18 CG1 VAL A 3 -3.687 3.033 1.165 1.00 21.34 C ATOM 19 CG2 VAL A 3 -1.885 4.782 1.039 1.00 19.65 C I can't reproduce this problem. I made a slight modification to the coordinates you posted to build CVAL so I could process the structure. It worked fine with version 4.0.7 (I don't have 4.0.4 installed any more). I would recommend that you upgrade to the latest version (4.5.1) instead of one that is over a year and a half old. The biggest benefit (aside from bug fixes) is that the Amber force fields are now natively supported, no more manual editing of residue names, termini, etc. If the problem persists (which it shouldn't, as I have also processed the file with version 4.5.1), then post again with the results. -Justin P.S. If you want to test what I did, here's the .pdb file I used. I opened yours in xLeap to build the termini. TITLE Giving Russians Opium May Alter Current Situation MODEL1 ATOM 1 N NGLYA 1 -5.201 9.673 -2.852 1.00 0.00 N ATOM 2 CA NGLYA 1 -3.724 9.368 -2.711 1.00 0.00 C ATOM 3 C NGLYA 1 -3.320 8.030 -3.324 1.00 0.00 C ATOM 4 O NGLYA 1 -4.164 7.323 -3.878 1.00 0.00 O ATOM 5 N ILE A 2 -2.065 7.644 -3.159 1.00 0.00 N ATOM 6 CA ILE A 2 -1.579 6.399 -3.716 1.00 0.00 C ATOM 7 CB ILE A 2 -0.037 6.325 -3.601 1.00 0.00 C ATOM 8 CG2 ILE A 2 0.397 6.250 -2.171 1.00 0.00 C ATOM 9 CG1 ILE A 2 0.494 5.122 -4.357 1.00 0.00 C ATOM 10 CD1 ILE A 2 2.013 5.071 -4.229 1.00 0.00 C ATOM 13 CD ILE A 2 1.946 5.193 -4.618 1.00 0.00 C ATOM 11 C ILE A 2 -2.254 5.174 -3.077 1.00 0.00 C ATOM 12 O ILE A 2 -2.629 4.249 -3.786 1.00 0.00 O ATOM 14 N CVALA 3 -2.487 5.202 -1.759 1.00 0.00 N ATOM 15 CA CVALA 3 -3.123 4.072 -1.065 1.00 0.00 C ATOM 16 CB CVALA 3 -3.225 4.312 0.465 1.00 0.00 C ATOM 17 CG1 CVALA 3 -3.687 3.033 1.165 1.00 0.00 C ATOM 18 CG2 CVALA 3 -1.885 4.782 1.039 1.00 0.00 C ATOM 19 C CVALA 3 -4.531 3.814 -1.605 1.00 0.00 C ATOM 20 OC1 CVALA 3 -4.954 2.670 -1.806 1.00 0.00 O ATOM 21 OC2 CVALA 3 -5.294 4.751 -1.829 1.00 0.00 O TER ENDMDL -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe
e: [gmx-users] Nucleotides for charmm port
gmx-users-requ...@gromacs.org wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. Nucleotides for charmm port (David Parcej) 2. Umbrella sampling question (Aswathy) 3. Re: WHAM (Justin A. Lemkul) 4. Re: Nucleotides for charmm port (Thomas Piggot) 5. Re: ARG Charmm gmx 4.5.1 (Thomas Piggot) 6. RE: ARG Charmm gmx 4.5.1 (Berk Hess) -- Message: 1 Date: Fri, 17 Sep 2010 11:44:08 +0200 From: David Parcej par...@biochem.uni-frankfurt.de Subject: [gmx-users] Nucleotides for charmm port To: gmx-users@gromacs.org Message-ID: 4c933868.4020...@biochem.uni-frankfurt.de Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi all, Has anybody managed to use ATP with the charmm27 ff in gromacs 4.5? The forcefield files are missing atom and bond types and angle information. This is available for charmm, but I have only found it in stream file and have no idea how to convert it. It should be possible (for someone smarter than me). cheers Dave Thank a lot Tom, it worked fine! Dave -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_hbond
hello, I have a trajectory generated by gromacs in which I excluded water and there is only protein, now I like to see how does the number of h_bond between water and protein change during the trajectory. In fact when I use g_hbond I can choose the water and protein but I was wondering where does the information about water come from?? thank you in advance for your time Fahimeh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_hbond
Fahimeh Baftizadeh Baghal wrote: hello, I have a trajectory generated by gromacs in which I excluded water and there is only protein, now I like to see how does the number of h_bond between water and protein change during the trajectory. In fact when I use g_hbond I can choose the water and protein but I was wondering where does the information about water come from?? Certainly you can choose whatever groups are present (either from default groups or from those in an index file), but I would imagine the command will either fail or simply identify that there are no hydrogen bond donors or acceptors within what would otherwise be water. If you have not saved the coordinates for water, you cannot run any command to analyze properties related to or involving water. -Justin thank you in advance for your time Fahimeh -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_hbond
On 9/17/10 5:37 PM, Justin A. Lemkul wrote: Fahimeh Baftizadeh Baghal wrote: hello, I have a trajectory generated by gromacs in which I excluded water and there is only protein, now I like to see how does the number of h_bond between water and protein change during the trajectory. In fact when I use g_hbond I can choose the water and protein but I was wondering where does the information about water come from?? Certainly you can choose whatever groups are present (either from default groups or from those in an index file), but I would imagine the command will either fail or simply identify that there are no hydrogen bond donors or acceptors within what would otherwise be water. If you have not saved the coordinates for water, you cannot run any command to analyze properties related to or involving water. In theory you could get an approximate number from analyzing what polar groups are not hydrogen bonded intramolecularly. There is not ready tool to do this. The quickest solution is probably to rerun the simulation. In most cases human time is more valuable than computer time. -Justin thank you in advance for your time Fahimeh -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_hbond
Thanks for the reply. In fact I had the trajectory with water but then I removed it to have smaller size of files. the point is that It didn't complain or crash when I was using that trajectory, choosing water in the groups selecting. but it didn't also generate any output. that is why I asked that ... Anyway since I have gro files time to time, I think I will cat all the gro file and use that for analysis of h_bond. Fahimeh --- On Fri, 9/17/10, David van der Spoel sp...@xray.bmc.uu.se wrote: From: David van der Spoel sp...@xray.bmc.uu.se Subject: Re: [gmx-users] g_hbond To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Friday, September 17, 2010, 9:37 PM On 9/17/10 5:37 PM, Justin A. Lemkul wrote: Fahimeh Baftizadeh Baghal wrote: hello, I have a trajectory generated by gromacs in which I excluded water and there is only protein, now I like to see how does the number of h_bond between water and protein change during the trajectory. In fact when I use g_hbond I can choose the water and protein but I was wondering where does the information about water come from?? Certainly you can choose whatever groups are present (either from default groups or from those in an index file), but I would imagine the command will either fail or simply identify that there are no hydrogen bond donors or acceptors within what would otherwise be water. If you have not saved the coordinates for water, you cannot run any command to analyze properties related to or involving water. In theory you could get an approximate number from analyzing what polar groups are not hydrogen bonded intramolecularly. There is not ready tool to do this. The quickest solution is probably to rerun the simulation. In most cases human time is more valuable than computer time. -Justin thank you in advance for your time Fahimeh -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_cluster cutoff
Hi, I am using g_cluster to analyse a trajectory (protein backbone): g_cluster -f traj.xtc -s topol.tpr -g cluster.log -skip 10 -cutoff 0.5 -fit -method linkage As a result I get almost hundred clusters. The plot of the RMSD against time for the same trajectory generated with g_rms shows a maximum RMSD just below 0.5 nm. Therefore, with a -cutoff of 0.5 nm, I would expect to find that the whole trajectory clusters into ONE cluster. Am I expecting something wrong or is there a problem with g_cluster ? (using Gromacs 4.07) Many thanks Andreas -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] force field to freeze/evaporate
Hi all, Sorry for my a bit off-top message. Does anybody know the force field model for water (polarizable/non-polarizable) that can reproduce the temperatures of liquid freezing/evaporation? For other common liquids, such models are also of interest. Thanks a lot. ~Vitaly -- Dr. Vitaly V. Chaban Department of Chemistry University of Rochester Rochester, NY 14642, United States of America -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] force field to freeze/evaporate
Hi, Of the cheap models I would think tip4p 2001 is the best. This has been parametrized to reproduce the phase diagram of water and does surprisingly well. Berk From: vvcha...@gmail.com Date: Fri, 17 Sep 2010 16:01:50 -0400 To: gmx-users@gromacs.org Subject: [gmx-users] force field to freeze/evaporate Hi all, Sorry for my a bit off-top message. Does anybody know the force field model for water (polarizable/non-polarizable) that can reproduce the temperatures of liquid freezing/evaporation? For other common liquids, such models are also of interest. Thanks a lot. ~Vitaly -- Dr. Vitaly V. Chaban Department of Chemistry University of Rochester Rochester, NY 14642, United States of America -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] unit conversions
Hi gmx-users, I would like to know the units conversion of epsilon, sigma (from non-bonded, Van der Waal interaction) from Charmm or MOIL to gromacs. Thank you. with regards, Rama -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] unit conversions
Ramachandran G wrote: Hi gmx-users, I would like to know the units conversion of epsilon, sigma (from non-bonded, Van der Waal interaction) from Charmm or MOIL to gromacs. Thank you. My guess would be that each of the respective manuals would discuss whatever unit conventions are utilized. As far as Gromacs is concerned, Chapter 4 contains information about such matters, as well as Table 5.2 (and sections nearby). -Justin with regards, Rama -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] ACE patch for CHARMM27
Hi GMXers, I am interested in simulating blocked peptides with CHARMM (and other force fields), using gromacs-4.5, and would appreciate some help from more experienced GROMACS users on details. To test things out I made a stab at creating an ACE N-terminal patch - this exists in OPLSAA, AMBER and CHARMM, so I added this to charmm27.ff/aminoacids.n.tdb: [ ACE ] [ add ] 1 2 CY NCA C C12.011000.51 1 2 OY CY NCA O15.99900 -0.51 1 1 CAY CY OY N CT3 12.01100 -0.27 3 4 HY CAY CY N HA1.00800 0.09 [ impropers ] CY CAY N OY N CY CA HN [ cmap ] CY N CA C +N Then built the top file with: pdb2gmx -f -inter ala5_alpha.pdb -p ala5.top -o ala5.gro -ff charmm27 -water tip3p -nochargegrp selecting ACE/CT2 as my terminal types The ala5.gro geometry looks fine, but in the ala5.top file there is no bond between atoms 2 and 7 (CY==OY in the patch), so the OY oxygen starts to drift off in EM and MD. All other bonds are generated. Can you tell me what is wrong here? Maybe somebody has already made a patch that works? I attach the ala5_alpha.pdb file Krzysztof -- Krzysztof Kuczera Departments of Chemistry and Molecular Biosciences The University of Kansas 2010 Malott Hall Lawrence, KS 66045 Tel: 785-864-5060 Fax: 785-864-5396 email: kkucz...@ku.edu http://oolung.chem.ku.edu/~kuczera/home.html ala5_alpha.pdb Description: Protein Databank data -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] ACE patch for CHARMM27
Krzysztof Kuczera wrote: Hi GMXers, I am interested in simulating blocked peptides with CHARMM (and other force fields), using gromacs-4.5, and would appreciate some help from more experienced GROMACS users on details. To test things out I made a stab at creating an ACE N-terminal patch - this exists in OPLSAA, AMBER and CHARMM, so I added this to charmm27.ff/aminoacids.n.tdb: [ ACE ] [ add ] 1 2 CY NCA C C12.011000.51 1 2 OY CY NCA O15.99900 -0.51 1 1 CAY CY OY N CT3 12.01100 -0.27 3 4 HY CAY CY N HA1.00800 0.09 [ impropers ] CY CAY N OY N CY CA HN [ cmap ] CY N CA C +N Then built the top file with: pdb2gmx -f -inter ala5_alpha.pdb -p ala5.top -o ala5.gro -ff charmm27 -water tip3p -nochargegrp selecting ACE/CT2 as my terminal types The ala5.gro geometry looks fine, but in the ala5.top file there is no bond between atoms 2 and 7 (CY==OY in the patch), so the OY oxygen starts to drift off in EM and MD. All other bonds are generated. Can you tell me what is wrong here? Maybe somebody has already made a patch that works? Nowhere in the .tdb entry is such a bond specified, nor can it be. The correct approach is to define .rtp entries, i.e.: http://lists.gromacs.org/pipermail/gmx-users/2010-July/052270.html -Justin I attach the ala5_alpha.pdb file Krzysztof -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] unit conversions
I understood from the gromacs manual the units for epsilon and sigma are KJ/mol and nm and the corresponding units in MOIL Kcal/mol and Angstom. But when i checked for some atoms, the epsilon values are not matching. i.e., for example i took the value of epsilon value of S from gromacs 1.8828 and divided by the conversion faction 4.184. The result is 0.45 but in MOIL the value is 0.25. I also checked some other atoms like K,Na,Cl... there also the values does not match. If anybody knows where i am making mistake please teach me. Thank you. with regards, Rama On Fri, Sep 17, 2010 at 2:20 PM, Justin A. Lemkul jalem...@vt.edu wrote: Ramachandran G wrote: Hi gmx-users, I would like to know the units conversion of epsilon, sigma (from non-bonded, Van der Waal interaction) from Charmm or MOIL to gromacs. Thank you. My guess would be that each of the respective manuals would discuss whatever unit conventions are utilized. As far as Gromacs is concerned, Chapter 4 contains information about such matters, as well as Table 5.2 (and sections nearby). -Justin with regards, Rama -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Postdoctoral Research Scholar, Department of Chemistry, University of Nevada, Reno. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] unit conversions
Ramachandran G wrote: I understood from the gromacs manual the units for epsilon and sigma are KJ/mol and nm and the corresponding units in MOIL Kcal/mol and Angstom. But when i checked for some atoms, the epsilon values are not matching. i.e., for example i took the value of epsilon value of S from gromacs 1.8828 and divided by the conversion faction 4.184. The result is 0.45 but in MOIL the value is 0.25. I also checked some other atoms like K,Na,Cl... there also the values does not match. Are you comparing the same force fields? According to the MOIL documentation, CHARMM is not implemented unless the user provides it. However, the epsilon value of OPLS-UA sulfur (1.046), when converted to MOIL units (kcal/mol), is 0.25, which I assume is where you're finding that value. -Justin If anybody knows where i am making mistake please teach me. Thank you. with regards, Rama On Fri, Sep 17, 2010 at 2:20 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Ramachandran G wrote: Hi gmx-users, I would like to know the units conversion of epsilon, sigma (from non-bonded, Van der Waal interaction) from Charmm or MOIL to gromacs. Thank you. My guess would be that each of the respective manuals would discuss whatever unit conventions are utilized. As far as Gromacs is concerned, Chapter 4 contains information about such matters, as well as Table 5.2 (and sections nearby). -Justin with regards, Rama -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Postdoctoral Research Scholar, Department of Chemistry, University of Nevada, Reno. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] unit conversions
Thank you Justin, You are right i am not comparing the same force field. But i am still curious to know the conversion factor for epsilon from MOIL to gromacs(charmm)force field. i.e., for sulfur epsilon value of 0.25 to 1.8828. Thank you. with regards, Rama On Fri, Sep 17, 2010 at 5:21 PM, Justin A. Lemkul jalem...@vt.edu wrote: Ramachandran G wrote: I understood from the gromacs manual the units for epsilon and sigma are KJ/mol and nm and the corresponding units in MOIL Kcal/mol and Angstom. But when i checked for some atoms, the epsilon values are not matching. i.e., for example i took the value of epsilon value of S from gromacs 1.8828 and divided by the conversion faction 4.184. The result is 0.45 but in MOIL the value is 0.25. I also checked some other atoms like K,Na,Cl... there also the values does not match. Are you comparing the same force fields? According to the MOIL documentation, CHARMM is not implemented unless the user provides it. However, the epsilon value of OPLS-UA sulfur (1.046), when converted to MOIL units (kcal/mol), is 0.25, which I assume is where you're finding that value. -Justin If anybody knows where i am making mistake please teach me. Thank you. with regards, Rama On Fri, Sep 17, 2010 at 2:20 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Ramachandran G wrote: Hi gmx-users, I would like to know the units conversion of epsilon, sigma (from non-bonded, Van der Waal interaction) from Charmm or MOIL to gromacs. Thank you. My guess would be that each of the respective manuals would discuss whatever unit conventions are utilized. As far as Gromacs is concerned, Chapter 4 contains information about such matters, as well as Table 5.2 (and sections nearby). -Justin with regards, Rama -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Postdoctoral Research Scholar, Department of Chemistry, University of Nevada, Reno. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Postdoctoral Research Scholar, Department of Chemistry, University of Nevada, Reno. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] unit conversions
Ramachandran G wrote: Thank you Justin, You are right i am not comparing the same force field. But i am still curious to know the conversion factor for epsilon from MOIL to gromacs(charmm)force field. i.e., for sulfur epsilon value of 0.25 to 1.8828. Thank you. If you are not comparing the same force fields, you are not likely to get the same answer. I thought I identified the fact that the value you are referring to corresponds to the MOIL implementation of OPLS-UA, which has no relationship whatsoever to the Gromacs implementation of CHARMM. Dividing by 4.184 is the correct conversion factor for kcal-kJ. -Justin with regards, Rama On Fri, Sep 17, 2010 at 5:21 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Ramachandran G wrote: I understood from the gromacs manual the units for epsilon and sigma are KJ/mol and nm and the corresponding units in MOIL Kcal/mol and Angstom. But when i checked for some atoms, the epsilon values are not matching. i.e., for example i took the value of epsilon value of S from gromacs 1.8828 and divided by the conversion faction 4.184. The result is 0.45 but in MOIL the value is 0.25. I also checked some other atoms like K,Na,Cl... there also the values does not match. Are you comparing the same force fields? According to the MOIL documentation, CHARMM is not implemented unless the user provides it. However, the epsilon value of OPLS-UA sulfur (1.046), when converted to MOIL units (kcal/mol), is 0.25, which I assume is where you're finding that value. -Justin If anybody knows where i am making mistake please teach me. Thank you. with regards, Rama On Fri, Sep 17, 2010 at 2:20 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Ramachandran G wrote: Hi gmx-users, I would like to know the units conversion of epsilon, sigma (from non-bonded, Van der Waal interaction) from Charmm or MOIL to gromacs. Thank you. My guess would be that each of the respective manuals would discuss whatever unit conventions are utilized. As far as Gromacs is concerned, Chapter 4 contains information about such matters, as well as Table 5.2 (and sections nearby). -Justin with regards, Rama -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Postdoctoral Research Scholar, Department of Chemistry, University of Nevada, Reno. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Postdoctoral Research Scholar, Department of Chemistry, University of Nevada, Reno. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar
Re: [gmx-users] unit conversions
Thank you for your clarification. Rama On Fri, Sep 17, 2010 at 5:49 PM, Justin A. Lemkul jalem...@vt.edu wrote: Ramachandran G wrote: Thank you Justin, You are right i am not comparing the same force field. But i am still curious to know the conversion factor for epsilon from MOIL to gromacs(charmm)force field. i.e., for sulfur epsilon value of 0.25 to 1.8828. Thank you. If you are not comparing the same force fields, you are not likely to get the same answer. I thought I identified the fact that the value you are referring to corresponds to the MOIL implementation of OPLS-UA, which has no relationship whatsoever to the Gromacs implementation of CHARMM. Dividing by 4.184 is the correct conversion factor for kcal-kJ. -Justin with regards, Rama On Fri, Sep 17, 2010 at 5:21 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Ramachandran G wrote: I understood from the gromacs manual the units for epsilon and sigma are KJ/mol and nm and the corresponding units in MOIL Kcal/mol and Angstom. But when i checked for some atoms, the epsilon values are not matching. i.e., for example i took the value of epsilon value of S from gromacs 1.8828 and divided by the conversion faction 4.184. The result is 0.45 but in MOIL the value is 0.25. I also checked some other atoms like K,Na,Cl... there also the values does not match. Are you comparing the same force fields? According to the MOIL documentation, CHARMM is not implemented unless the user provides it. However, the epsilon value of OPLS-UA sulfur (1.046), when converted to MOIL units (kcal/mol), is 0.25, which I assume is where you're finding that value. -Justin If anybody knows where i am making mistake please teach me. Thank you. with regards, Rama On Fri, Sep 17, 2010 at 2:20 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Ramachandran G wrote: Hi gmx-users, I would like to know the units conversion of epsilon, sigma (from non-bonded, Van der Waal interaction) from Charmm or MOIL to gromacs. Thank you. My guess would be that each of the respective manuals would discuss whatever unit conventions are utilized. As far as Gromacs is concerned, Chapter 4 contains information about such matters, as well as Table 5.2 (and sections nearby). -Justin with regards, Rama -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Postdoctoral Research Scholar, Department of Chemistry, University of Nevada, Reno. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Postdoctoral Research Scholar, Department of Chemistry, University of Nevada,
