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] Position restraining of ions.
You can copy the part regarding the certain ion type from ions.itp to a separate itp file and #include that itp file into a top file. Then #include the position restraint file that has restraints for only one ion of that type at the end of that new itp file. By this manner you can even split a group of same ions (for example, some potassium ions are restrained and others are not) by making separate itp files for potassium ions in which you specify different [ moleculetype ] names for each file and doing that accordingly at the [ molecules ] table at the end of a top file. Of course, when you split groups you need to know the positions of ions of interest in a system structural file (gro or pdb), as they need to be listed in the same order in the [ molecules ] table. Gordan On 7/16/2015 2:36 AM, Justin Lemkul wrote: On 7/15/15 11:53 AM, anu chandra wrote: Dear Gromcacs users, I have carried out 25 ns simulation of membrane-protein systems. Now, I would like to do position restrain of ions for the next 1-2 ns. I have KCl in my system. I used ' genrestr ' for generating the position restrain for ions using the following command - genrestr -f md50.gro -o ions-rest.itp I have included ions-rest.itp in the .top file with proper ' ifdef ' term as mention in tutorials. Unfortunately, the grommp shows error message - Atom index (2) in position_restraints out of bounds (1-1). This probably means that you have inserted topology section position_restraints in a part belonging to a different molecule than you intended to . I have seen from Gromcas mail list that many faced similar issues and this usually comes from the mismatch in atom indices. Unfortunately, I could not find complete solution for it yet. Few queries in this regard are, 1. How can I generate a position restrain file for ions or any set of molecules in the system? my topology file have following hierarchy, ; This is a standalone topology file ; ; Created by: ; GROMACS: gmx pdb2gmx, VERSION 5.0.4 ; Executable: /usr/local/gromacs/bin/gmx ; Library dir: /usr/local/gromacs/share/gromacs/top ; Command line: ; gmx pdb2gmx -f step5_IP3R.pdb -ter ; Force field was read from the standard Gromacs share directory. ; ; Include forcefield parameters #include charmm36-jun2015.ff/forcefield.itp ; Include chain topologies #include topol_Protein.itp #include topol_Protein2.itp #include topol_Protein3.itp #include topol_Protein4.itp #include POPC.itp ; Include water topology #include charmm36-jun2015.ff/tip3p.itp ; Include topology for ions #include charmm36-jun2015.ff/ions.itp [ system ] ; Name Titile [ molecules ] ; Compound#mols Protein 1 Protein21 Protein31 Protein41 POPC 295 POT 85 CL 122 SOL24892 2. Where all I can use the .itp file for a particular group generate with ' genrestr' command? Restraints are applied on a per-moleculetype basis; hence genrestr is very limited in what it can do (multiple molecules won't work without considerable effort). The only way to restrain the ions within this setup is to modify ions.itp to specify restraints within the relevant [moleculetype] directives. -Justin -- 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] Position restraining of ions.
#ifdef REST_ON #include POT_rest.itp #endif should go at the end of POT_rest.itp file and #ifdef REST_ON #include CL_rest.itp #endif should go at the end of CL.itp file. The restraint you listed restraints the first atom of every molecule of the type stated in the corresponding itp file. Since potassium and chloride ions are monoatomic, that should work fine. Elsewise, you can just put the line #include ionX_rest.itp at the end of the ionX.itp file which will turn on restraints automatically without having to define -DPOSIONX keyword in mdp file. Gordan On 7/16/2015 11:51 AM, anu chandra wrote: Hi, Thanks for your prompt reply. I have modified the top file as shown below. Though it looks working fine for me, can you please have quick look into it. *** r ; Force field was read from the standard Gromacs share directory. ; ; Include forcefield parameters #include charmm36-jun2015.ff/forcefield.itp ; Include chain topologies #include topol_Protein.itp #include topol_Protein2.itp #include topol_Protein3.itp #include topol_Protein4.itp #include POPC.itp #include POT.itp #ifdef REST_ON #include POT_rest.itp #endif #include CL.itp #ifdef REST_ON #include CL_rest.itp #endif ; Include water topology #include charmm36-jun2015.ff/tip3p.itp [ system ] ; Name Titile [ molecules ] ; Compound#mols Protein 1 Protein21 Protein31 Protein41 POPC 295 POT 85 CL 122 SOL 24892 ** And my POT_rest.itp and CL_rest have similar format as follows, *** ; position restraints for POT of GROningen MAchine for Chemical Simulation [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 *** and I have ' define = -DREST_ON ' in mdp file. Hope what I am doing is right? Many thanks Anu On Thu, Jul 16, 2015 at 7:32 AM, Gordan Horvat ghor...@chem.pmf.hr wrote: You can copy the part regarding the certain ion type from ions.itp to a separate itp file and #include that itp file into a top file. Then #include the position restraint file that has restraints for only one ion of that type at the end of that new itp file. By this manner you can even split a group of same ions (for example, some potassium ions are restrained and others are not) by making separate itp files for potassium ions in which you specify different [ moleculetype ] names for each file and doing that accordingly at the [ molecules ] table at the end of a top file. Of course, when you split groups you need to know the positions of ions of interest in a system structural file (gro or pdb), as they need to be listed in the same order in the [ molecules ] table. Gordan On 7/16/2015 2:36 AM, Justin Lemkul wrote: On 7/15/15 11:53 AM, anu chandra wrote: Dear Gromcacs users, I have carried out 25 ns simulation of membrane-protein systems. Now, I would like to do position restrain of ions for the next 1-2 ns. I have KCl in my system. I used ' genrestr ' for generating the position restrain for ions using the following command - genrestr -f md50.gro -o ions-rest.itp I have included ions-rest.itp in the .top file with proper ' ifdef ' term as mention in tutorials. Unfortunately, the grommp shows error message - Atom index (2) in position_restraints out of bounds (1-1). This probably means that you have inserted topology section position_restraints in a part belonging to a different molecule than you intended to . I have seen from Gromcas mail list that many faced similar issues and this usually comes from the mismatch in atom indices. Unfortunately, I could not find complete solution for it yet. Few queries in this regard are, 1. How can I generate a position restrain file for ions or any set of molecules in the system? my topology file have following hierarchy, ; This is a standalone topology file ; ; Created by: ; GROMACS: gmx pdb2gmx, VERSION 5.0.4 ; Executable: /usr/local/gromacs/bin/gmx ; Library dir: /usr/local/gromacs/share/gromacs/top ; Command line: ; gmx pdb2gmx -f step5_IP3R.pdb -ter ; Force field was read from the standard Gromacs share directory. ; ; Include forcefield parameters #include charmm36-jun2015.ff/forcefield.itp ; Include chain topologies #include topol_Protein.itp #include topol_Protein2.itp #include topol_Protein3.itp #include topol_Protein4.itp #include POPC.itp ; Include water topology #include charmm36-jun2015.ff/tip3p.itp ; Include topology for ions #include charmm36-jun2015
Re: [gmx-users] Position restraining of ions.
I should correct myself. Your top file should work too, because grompp assigns certain restraints included in top file to molecules of type defined in the first itp file found above the line that includes these restraints. http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_restraints_out_of_bounds Alternatively, you can put the #ifdef REST_ON [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif section in your top file below the line that includes the ion group itp file, or in the itp file of each ion group you want restrained. Gordan On 7/16/2015 13:47 PM, Justin Lemkul wrote: On 7/16/15 6:22 AM, Gordan Horvat wrote: #ifdef REST_ON #include POT_rest.itp #endif should go at the end of POT_rest.itp file and #ifdef REST_ON #include CL_rest.itp #endif should go at the end of CL.itp file. The restraint you listed restraints the first atom of every molecule of the type stated in the corresponding itp file. Since potassium and chloride ions are monoatomic, that should work fine. Neither of the #ifdefs have to be in the actual .itp files. They must correspond to the [moleculetype], and since they are appropriately listed consecutively here, this approach works fine. Elsewise, you can just put the line #include ionX_rest.itp at the end of the ionX.itp file which will turn on restraints automatically without having to define -DPOSIONX keyword in mdp file. This is dangerous because then the restraints are *always* on, which is usually undesirable. If you forget to modify the files if conditions change, then run a long simulation... -Justin -- 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.
