[gmx-users] CHarmm and popc membrane
Hi, > I still don't see it (see below), is this [no]chargegrp new in the cvs ? > I'm pretty sure that you're not referring to [no]lys, etc. Yes, that seems to be the case indeed. I've got it in my 'cvs' installation but not in my 4.0.7. /Pär-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] CHarmm and popc membrane
That's why I said if you know what you're doing :) ok, fair enough. The name flag is listed as [no]chargegrp I still don't see it (see below), is this [no]chargegrp new in the cvs ? I'm pretty sure that you're not referring to [no]lys, etc. $ /scratch/cneale/GPC/exe/intel/gromacs-4.0.7/exec/bin/pdb2gmx -h > z 2>&1; cat z|grep charge encads Encad all-atom force field, using scaled-down vacuum charges encadv Encad all-atom force field, using full solvent charges -[no]ter bool no Interactive termini selection, iso charged -[no]lys bool no Interactive Lysine selection, iso charged -[no]arg bool no Interactive Arganine selection, iso charged -[no]asp bool no Interactive Aspartic Acid selection, iso charged -[no]glu bool no Interactive Glutamic Acid selection, iso charged ## Chris. -- original message -- Hi Chris, / />/ I believe that the latest response had the wrong subject, so I am />/ changing it back. />/ />/ Pär, two comments: />/ First, does that option really exist? />/ />/ $ /scratch/cneale/GPC/exe/intel/gromacs-4.0.7/exec/bin/pdb2gmx -h > z />/ 2>&1; cat z|grep nochargegrp|wc -l />/ /The name flag is listed as [no]chargegrp / />/ Second, I am not entirely convinced that one can discount the need for />/ gromacs-style charge groups. When CHARMM includes an atom in the />/ cutoff, it includes the entire charge group, but that doesn't mean the />/ algorithms of CHARMM and gromacs are entirely the same /That's why I said if you know what you're doing :) / />/ I gather that the large charge group listed below is the one that is />/ spurring the message: />/ />/ GROUP ! H31 />/ ATOM NNTL-0.60 ! | />/ ATOM C11 CTL2 -0.10 ! H33-C13-H32 />/ ATOM C12 CTL5 -0.35 ! | />/ ATOM C13 CTL5 -0.35 ! H21 | H43 />/ ATOM C14 CTL5 -0.35 !|| | />/ ATOM H11 HL 0.25 ! H22-C12---N---C14-H42 (+) />/ ATOM H12 HL 0.25 !|| | />/ ATOM H21 HL 0.25 !H23 | H41 />/ ATOM H22 HL 0.25 ! | />/ ATOM H23 HL 0.25 ! | />/ ATOM H31 HL 0.25 ! | />/ ATOM H32 HL 0.25 ! H11-C11-H12 />/ ATOM H33 HL 0.25 ! | />/ ATOM H41 HL 0.25 ! | />/ ATOM H42 HL 0.25 ! | />/ ATOM H43 HL 0.25 ! | /Yes, and probably one charge group in the arginine residue(s). /Pär -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
RE: [gmx-users] CHarmm and popc membrane (response to "Missing Residues are list ind pdb file")
Hi Chris, > > I believe that the latest response had the wrong subject, so I am > changing it back. > > Pär, two comments: > First, does that option really exist? > > $ /scratch/cneale/GPC/exe/intel/gromacs-4.0.7/exec/bin/pdb2gmx -h > z > 2>&1; cat z|grep nochargegrp|wc -l > The name flag is listed as [no]chargegrp > > Second, I am not entirely convinced that one can discount the need for > gromacs-style charge groups. When CHARMM includes an atom in the > cutoff, it includes the entire charge group, but that doesn't mean the > algorithms of CHARMM and gromacs are entirely the same That's why I said if you know what you're doing :) > > I gather that the large charge group listed below is the one that is > spurring the message: > > GROUP ! H31 > ATOM NNTL-0.60 ! | > ATOM C11 CTL2 -0.10 ! H33-C13-H32 > ATOM C12 CTL5 -0.35 ! | > ATOM C13 CTL5 -0.35 ! H21 | H43 > ATOM C14 CTL5 -0.35 !|| | > ATOM H11 HL 0.25 ! H22-C12---N---C14-H42 (+) > ATOM H12 HL 0.25 !|| | > ATOM H21 HL 0.25 !H23 | H41 > ATOM H22 HL 0.25 ! | > ATOM H23 HL 0.25 ! | > ATOM H31 HL 0.25 ! | > ATOM H32 HL 0.25 ! H11-C11-H12 > ATOM H33 HL 0.25 ! | > ATOM H41 HL 0.25 ! | > ATOM H42 HL 0.25 ! | > ATOM H43 HL 0.25 ! | Yes, and probably one charge group in the arginine residue(s). /Pär-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] CHarmm and popc membrane (response to "Missing Residues are list ind pdb file")
Hi Stefan and Pär, I believe that the latest response had the wrong subject, so I am changing it back. Pär, two comments: First, does that option really exist? $ /scratch/cneale/GPC/exe/intel/gromacs-4.0.7/exec/bin/pdb2gmx -h > z 2>&1; cat z|grep nochargegrp|wc -l Second, I am not entirely convinced that one can discount the need for gromacs-style charge groups. When CHARMM includes an atom in the cutoff, it includes the entire charge group, but that doesn't mean the algorithms of CHARMM and gromacs are entirely the same, especially with respect to: "Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large charge groups can lead to serious cut-off artifacts." I admit that it has been 3 years since I used CHARMM, but as I recall the requirement for pair interactions to count within the cutoff is only that one atom within the charge group is close enough, whereas the gromacs warning indicates that in gromacs the interaction is only counted when the center of mass of the charge groups are also within the cutoff. Any charmmers out there that can clear this up? I did some searching on their archives but I was blocked after 3 searches unless I logged in (ugh!). I gather that the large charge group listed below is the one that is spurring the message: GROUP ! H31 ATOM NNTL-0.60 ! | ATOM C11 CTL2 -0.10 ! H33-C13-H32 ATOM C12 CTL5 -0.35 ! | ATOM C13 CTL5 -0.35 ! H21 | H43 ATOM C14 CTL5 -0.35 !|| | ATOM H11 HL 0.25 ! H22-C12---N---C14-H42 (+) ATOM H12 HL 0.25 !|| | ATOM H21 HL 0.25 !H23 | H41 ATOM H22 HL 0.25 ! | ATOM H23 HL 0.25 ! | ATOM H31 HL 0.25 ! | ATOM H32 HL 0.25 ! H11-C11-H12 ATOM H33 HL 0.25 ! | ATOM H41 HL 0.25 ! | ATOM H42 HL 0.25 ! | ATOM H43 HL 0.25 ! | -- original message -- Hi, Note, that this is indeed the size of the charge groups in the CHARMM force field. You could run pdb2gmx -nochargegrp if you know what you're doing. Regards, Pär Bjelkmar I think the notes from grompp are pretty clear. You need to redivide your charge groups so that they contain fewer atoms. You can do this in the .top or .itp file and you can find out how to do that in the manual. Feel free to post your original and charge-group-modified topologies back here if you want people to take a look at them. Chris. -- original message -- I am trying to equilibrate a POPC membrane with 128 POPC molecules, but grompp gives out the following notes and minimization with mdrun does not work. The output on screen of mdrun comes out like this: Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax < 10. Potential Energy = 1.4422483e+17 Maximum force =inf on atom 4082 Norm of force =inf And grompp notes are: NOTE 2 [file topol.top, line unknown]: The largest charge group contains 12 atoms. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] CHarmm and popc membrane
I think the notes from grompp are pretty clear. You need to redivide your charge groups so that they contain fewer atoms. You can do this in the .top or .itp file and you can find out how to do that in the manual. Feel free to post your original and charge-group-modified topologies back here if you want people to take a look at them. Chris. -- original message -- I am trying to equilibrate a POPC membrane with 128 POPC molecules, but grompp gives out the following notes and minimization with mdrun does not work. The output on screen of mdrun comes out like this: Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax < 10. Potential Energy = 1.4422483e+17 Maximum force =inf on atom 4082 Norm of force =inf And grompp notes are: NOTE 2 [file topol.top, line unknown]: The largest charge group contains 12 atoms. Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large charge groups can lead to serious cut-off artifacts. For efficiency and accuracy, charge group should consist of a few atoms. For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc. NOTE 3 [file topol.top, line unknown]: The largest charge group contains 16 atoms. Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large charge groups can lead to serious cut-off artifacts. For efficiency and accuracy, charge group should consist of a few atoms. For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc. Here is my minimization mdp file, I have used the first one with PME but then changed to Reaction-field and no PBC (just as curiosity to see if it worked). integrator= steep emtol= 1000.0 emstep = 0.01 nsteps= 5 nstlist= 1 ns_type= grid rlist= 1.2 coulombtype= PME rcoulomb= 1.2 rvdw= 1.2 pbc= xyz -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] CHarmm and popc membrane
I am trying to equilibrate a POPC membrane with 128 POPC molecules, but grompp gives out the following notes and minimization with mdrun does not work. The output on screen of mdrun comes out like this: Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax < 10. Potential Energy = 1.4422483e+17 Maximum force =inf on atom 4082 Norm of force =inf And grompp notes are: NOTE 2 [file topol.top, line unknown]: The largest charge group contains 12 atoms. Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large charge groups can lead to serious cut-off artifacts. For efficiency and accuracy, charge group should consist of a few atoms. For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc. NOTE 3 [file topol.top, line unknown]: The largest charge group contains 16 atoms. Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large charge groups can lead to serious cut-off artifacts. For efficiency and accuracy, charge group should consist of a few atoms. For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc. Here is my minimization mdp file, I have used the first one with PME but then changed to Reaction-field and no PBC (just as curiosity to see if it worked). integrator= steep emtol= 1000.0 emstep = 0.01 nsteps= 5 nstlist= 1 ns_type= grid rlist= 1.2 coulombtype= PME rcoulomb= 1.2 rvdw= 1.2 pbc= xyz Thank you -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
