Re: [gmx-users] Re: Re: Does GMX compute coulomb interaction between oxygen and hydrogen in SPC water model?
xuji wrote: Thank you for your help! Mark Abraham. I make a mistake about the codes which compute the coulomb interactions in nb_generic.c yestoday. Sorry for it. And I find that there're some difference between the tabulated coulomb function and Vanilla cutoff coulomb interaction function. So waht does contribution to the difference? Can I use the cut-off function instead of the tabulated function? And how can I get the parameters in tabulated function? Please start by reading the relevant manual sections. Mark ___ 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: Fwd: [gmx-users] scripts to generate topology CG
On Fri, Oct 23, 2009 at 5:32 PM, Justin A. Lemkul jalem...@vt.edu wrote: Francesco Pietra wrote: grep W solvated.gro | wc -l and use that number in the topology? I forgot to add that the graphic program uses the above grep command, I don't understand this statement. giving the same number of W as the line command. The number of DCCP is diminished by those deleted in inserting the protein, but the grompp command complains that .gro does not matches .top. If no further water is added graphically, everything works. This is where exact commands (in sequence) really help, or at least a stepwise procedure. Are you adding a protein into a box that contains DCCP+water, or are you inserting the protein into DCCP, then adding water? What is the exact error that grompp is giving you? That the number of coordinates don't match? atom names don't match? What I did follows. I am using the actual filenames and page numbers for my reference. (1) getting mod21.cg.pdb from mod21.pdb by using the martini awk script (p. 4). (2) getting mod21.itp by using dssp, fasta, seq2itp.pl (p. 4). (3) downloading dppc_bilayer.gro, editconf to get dppc_bilayer.pdb (p. 4). (4) inserting the pore region of the cg protein into the bilayer in the obvious orientation, then removing all dppc superimposed to the protein plus an extra margin of 10A, to get mod21.aligned.pdb and dppc.aligned.pdb (according to as described for all-atoms in the paper I referred to in this thread) (p. 4) (5) genbox -cp mod21.aligned.pdb -cs dppc.aligned.pdb -box 11 11 11 -o mod21+dccp.box.pdb resulted in the protein at a corner of the cubic box. This is probably because I was using a homology model, i.e., there was no CRYSTAL record. It was nonetheless surprising because the two .pdb files to combine had the same box size (p. 5). (6) Cut-and-paste adding mod21.aligned.pdb to dppc.aligned.pdb resulted in a correct insertion of the pore region into the bilayer, the latter correctly oriented. Filename dppc+mod21.pdb (p. 6). The bilayer originally was made of 128 dppc and 2000 W. After insertion of the protein, the system was 1 multimeric protein, 85 dppc and 1767 W (taking into account that there are 12 atoms per dppc). (7) genbox -cp dppc+mod21.pdb -cs water-1bar.303K.gro -box 11 20 11 -o dppc+mod21+W.box.pdb resulted in the protein at a corner of the solvating box, which only comprised the pore region inserted into the bilayer. I.e., the large non-pore region of the protein was not solvated. On making the box bigger and bigger also the non-pore region was solvated but the pore region exited the bilayer and entered the water region. Which situation could not be accepted (pp. 8-9). I was unable to detect whether I was using wrong commands with genbox, and therefore I abandoned genbox. (8) Starting from dppc+mod21.pdb (from step 6) I tried solvating the non-pore region of the protein-dppc ensemble by adding a preformed box of water (that is, using the methodology of step 4). Thus, dppc+mod21.pd was aligned with a water box of 5400 W, removing all W superimposed to the non-pore region of mod21+dppc, plus a margin of 10A. The ensemble (filename dppc+mod21+W.gro) opens correctly in VMD (or as corresponding .pdb file in CHIMERA), that is, the non-pore region is solvated (pp. 11-12). In my hands, the .pdb file describing this ensemble did not allow to generate a .tpr file. The ensemble was made of Protein 1 (multimeric) DPPC 85 W 6008 which data were used for the .top file. Command $ grompp -f minimize.mdp -c dppc+mod21+W.gro -p dppc+mod21+W.top -o minimize.tpr resulted in error: number of coordinates in coordinate file (dppc+mod21+W.gro 5662) does not match topology (dppc+mod21+W.top, 9903) (p. 19). (9) Starting directly from dppc+mod21.pdb (from step 6), commad $ genbox -cp dppc+mod21.pdb -box 10 17 10 -o dppc+mod21.gro 5662 atoms in 3122 residues Volume: 1700 nm^3 Density: 99.5996 SOL: 0 followed by command $ grompp -f minimize.mdp -c dppc+mod21.gro -p dppc+mod21.top -o minimize.tpr where, for the .top file, [molecule] Protein 1 DPPC 85 W 1767 (derived as indicated at step 6) generated correctly the .tpr file (p. 20). ... I hope to have illustrated in sufficient details the procedure so as my mistakes could be detected. thanks for help francesco -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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 list gmx-us...@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
Re: Fwd: [gmx-users] scripts to generate topology CG
Francesco Pietra wrote: On Fri, Oct 23, 2009 at 5:32 PM, Justin A. Lemkul jalem...@vt.edu wrote: Francesco Pietra wrote: grep W solvated.gro | wc -l and use that number in the topology? I forgot to add that the graphic program uses the above grep command, I don't understand this statement. giving the same number of W as the line command. The number of DCCP is diminished by those deleted in inserting the protein, but the grompp command complains that .gro does not matches .top. If no further water is added graphically, everything works. This is where exact commands (in sequence) really help, or at least a stepwise procedure. Are you adding a protein into a box that contains DCCP+water, or are you inserting the protein into DCCP, then adding water? What is the exact error that grompp is giving you? That the number of coordinates don't match? atom names don't match? What I did follows. I am using the actual filenames and page numbers for my reference. (1) getting mod21.cg.pdb from mod21.pdb by using the martini awk script (p. 4). (2) getting mod21.itp by using dssp, fasta, seq2itp.pl (p. 4). (3) downloading dppc_bilayer.gro, editconf to get dppc_bilayer.pdb (p. 4). (4) inserting the pore region of the cg protein into the bilayer in the obvious orientation, then removing all dppc superimposed to the protein plus an extra margin of 10A, to get mod21.aligned.pdb and dppc.aligned.pdb (according to as described for all-atoms in the paper I referred to in this thread) (p. 4) (5) genbox -cp mod21.aligned.pdb -cs dppc.aligned.pdb -box 11 11 11 -o mod21+dccp.box.pdb resulted in the protein at a corner of the cubic box. This is probably because I was using a homology model, i.e., there was no CRYSTAL record. It was nonetheless surprising because the two .pdb files to combine had the same box size (p. 5). Box manipulation can be tricky. I would recommend doing the alignment with editconf, for example, to place the bilayer and protein centers at the center of the box, you would issue: editconf -f mod21.aligned.pdb -o mod21.aligned.center.pdb -c -box 11 -bt cubic And analogously for the bilayer. If the center must be shifted relative to the box center, you can supply to exact coordinates with editconf -center. (6) Cut-and-paste adding mod21.aligned.pdb to dppc.aligned.pdb resulted in a correct insertion of the pore region into the bilayer, the latter correctly oriented. Filename dppc+mod21.pdb (p. 6). The bilayer originally was made of 128 dppc and 2000 W. After insertion of the protein, the system was 1 multimeric protein, 85 dppc and 1767 W (taking into account that there are 12 atoms per dppc). (7) genbox -cp dppc+mod21.pdb -cs water-1bar.303K.gro -box 11 20 11 -o dppc+mod21+W.box.pdb resulted in the protein at a corner of the solvating box, which only comprised the pore region inserted into the bilayer. I.e., the large non-pore region of the protein was not solvated. On making the box bigger and bigger also the non-pore region was solvated but the pore region exited the bilayer and entered the water region. Which situation could not be accepted (pp. 8-9). I think genbox is inducing this effect because it is trying to assemble your system within the -box you have defined. I am not aware of any known issues with using genbox -box, but as a matter of routine, I always define the box with editconf prior to running genbox. Again, I don't know of anything that is broken about genbox, but it would be worthwhile to eliminate this as a potential problem. I was unable to detect whether I was using wrong commands with genbox, and therefore I abandoned genbox. (8) Starting from dppc+mod21.pdb (from step 6) I tried solvating the non-pore region of the protein-dppc ensemble by adding a preformed box of water (that is, using the methodology of step 4). Thus, dppc+mod21.pd was aligned with a water box of 5400 W, removing all W superimposed to the non-pore region of mod21+dppc, plus a margin of 10A. The ensemble (filename dppc+mod21+W.gro) opens correctly in VMD (or as corresponding .pdb file in CHIMERA), that is, the non-pore region is solvated (pp. 11-12). In my hands, the .pdb file describing this ensemble did not allow to generate a .tpr file. The ensemble was made of Protein 1 (multimeric) DPPC 85 W 6008 which data were used for the .top file. Command $ grompp -f minimize.mdp -c dppc+mod21+W.gro -p dppc+mod21+W.top -o minimize.tpr resulted in error: number of coordinates in coordinate file (dppc+mod21+W.gro 5662) does not match topology (dppc+mod21+W.top, 9903) (p. 19). Can you post the first and last few lines of dppc+mod21+W.gro (i.e., head dppc+mod21+W.gro and tail dppc+mod21+W.gro)? -Justin (9) Starting directly from dppc+mod21.pdb (from step 6), commad $ genbox -cp dppc+mod21.pdb -box 10 17 10 -o dppc+mod21.gro 5662 atoms in 3122 residues Volume: 1700 nm^3 Density: 99.5996
Re: [gmx-users] Which membrane result is more reliable?
DMPE.itp file as attached [ moleculetype ] ; Name nrexcl DMPE 3 [ atoms ] ; nrtype resnr residuatomcgnrcharge mass 1 H 1DMPE H1 0 0.4000 1.0080; qtot:0.36 2 H 1DMPE H2 0 0.4000 1.0080; qtot:0.72 3 H 1DMPE H3 0 0.4000 1.0008; qtot:1.08 4 LNL 1DMPE N4 0-0.5000 14.0067 ; qtot:0.76 5 LH2 1DMPE C5 0 0.3000 14.0270; qtot:1.0 6 LC2 1DMPE C6 1 0.4000 14.0270; qtot:1.0 7 LOS 1DMPE O7 1-0.800 15.9994; qtot:0.54 8 LP1DMPE P8 1 1.700 30.9738; qtot:2.3 9 LOM 1DMPE O9 1-0.800 15.9994; qtot:1.5 10 LOM 1DMPE O10 1-0.800 15.9994; qtot:0.7 11 LOS 1DMPE O11 1-0.700 15.9994; qtot:0 12 LC2 1DMPE C12 2 0.400 14.0270; qtot:0.08 13 LH1 1DMPE C13 2 0.300 13.0190; qtot:0.52 14 LOS 1DMPE O14 2-0.700 15.9994; qtot:-0.14 15 LC 1DMPE C15 2 0.7000 12.0110; qtot:0.56 16 LO 1DMPE O16 2-0.700 15.9994; qtot:0.0 17 LP2 1DMPE C17 3 0.0 14.0270; qtot: 18 LP2 1DMPE C18 4 014.0270; qtot: 19 LP2 1DMPE C19 5 014.0270; qtot: 20 LP2 1DMPE C20 6 014.0270; qtot: 21 LP2 1DMPE C21 7 014.0270; qtot: 22 LP2 1DMPE C22 8 014.0270; qtot: 23 LP2 1DMPE C23 9 014.0270; qtot: 24 LP2 1DMPE C24 10 014.0270; qtot: 25 LP2 1DMPE C25 11 014.0270; qtot: 26 LP2 1DMPE C26 12 014.0270; qtot: 27 LP2 1DMPE C27 13 014.0270; qtot: 28 LP2 1DMPE C28 14 014.0270; qtot: 29 LP3 1DMPE C29 15 015.0350; qtot: 30 LC2 1DMPE C32 16 0.5014.0270; qtot: 31 LOS 1DMPE O33 16 -0.7015.9994; qtot: 32 LC 1DMPE C34 16 0.8012.0110; qtot: 33 LO 1DMPE O35 16 -0.6015.9994; qtot: 34 LP2 1DMPE C36 17 014.0270; qtot: 35 LP2 1DMPE C37 18 014.0270; qtot: 36 LP2 1DMPE C38 19 014.0270; qtot: 37 LP2 1DMPE C39 20 014.0270; qtot: 38 LP2 1DMPE C40 21 014.0270; qtot: 39 LP2 1DMPE C41 22 014.0270; qtot: 40 LP2 1DMPE C42 23 014.0270; qtot: 41 LP2 1DMPE C43 24 014.0270; qtot: 42 LP2 1DMPE C44 25 014.0270; qtot: 43 LP2 1DMPE C45 26 014.0270; qtot: 44 LP2 1DMPE C46 27 014.0270; qtot: 45 LP2 1DMPE C47 28 014.0270; qtot: 46 LP3 1DMPE C48 29 015.0350; tail: [ bonds ] ; aiaj funct 1 4 1 0.1E+00 0.37450E+06 2 4 1 0.1E+00 0.37450E+06 3 4 1 0.1E+00 0.37450E+06 4 5 1 0.14700E+00 0.37660E+06 5 6 1 0.15300E+00 0.33470E+06 6 7 1 0.14300E+00 0.25100E+06 7 8 1 0.16100E+00 0.25100E+06 8 9 1 0.14800E+00 0.37660E+06 8 10 1 0.14800E+00 0.37660E+06 8 11 1 0.16100E+00 0.25100E+06 11 12 1 0.14300E+00 0.25100E+06 12 13 1 0.15300E+00 0.33470E+06 13 14 1 0.14350E+00 0.25100E+06 13 30 1 0.15300E+00 0.33470E+06 14 15 1 0.13600E+00 0.37660E+06 15 16 1 0.12300E+00 0.50210E+06 15 17 1 0.15300E+00 0.33470E+06 17 18 1 0.15300E+00 0.33470E+06 18 19 1 0.15300E+00 0.33470E+06 19 20
Re: [gmx-users] Which membrane result is more reliable?
There is nothing remarkable here, it looks to be a few changes in atom type relative to DMPC, a procedure that I know has been used successfully for DPPC:DPPE mixtures: dx.doi.org/10.1529/biophysj.105.076596 I stand by my previous reply. When analyzing your data, you have to consider the innately different chemistry between DMPC and DMPE, particularly the headgroups. I also would not draw any conclusions about the data generated without a good set of controls (lipid only, no protein). I would also not expect two different lipids to have the same influence on a bound protein. -Justin Kirill Bessonov wrote: DMPE.itp file as attached [ moleculetype ] ; Name nrexcl DMPE 3 [ atoms ] ; nrtype resnr residuatomcgnrcharge mass 1 H 1DMPE H1 0 0.4000 1.0080; qtot:0.36 2 H 1DMPE H2 0 0.4000 1.0080; qtot:0.72 3 H 1DMPE H3 0 0.4000 1.0008; qtot:1.08 4 LNL 1DMPE N4 0-0.5000 14.0067 ; qtot:0.76 5 LH2 1DMPE C5 0 0.3000 14.0270; qtot:1.0 6 LC2 1DMPE C6 1 0.4000 14.0270; qtot:1.0 7 LOS 1DMPE O7 1-0.800 15.9994; qtot:0.54 8 LP1DMPE P8 1 1.700 30.9738; qtot:2.3 9 LOM 1DMPE O9 1-0.800 15.9994; qtot:1.5 10 LOM 1DMPE O10 1-0.800 15.9994; qtot:0.7 11 LOS 1DMPE O11 1-0.700 15.9994; qtot:0 12 LC2 1DMPE C12 2 0.400 14.0270; qtot:0.08 13 LH1 1DMPE C13 2 0.300 13.0190; qtot:0.52 14 LOS 1DMPE O14 2-0.700 15.9994; qtot:-0.14 15 LC 1DMPE C15 2 0.7000 12.0110; qtot:0.56 16 LO 1DMPE O16 2-0.700 15.9994; qtot:0.0 17 LP2 1DMPE C17 3 0.0 14.0270; qtot: 18 LP2 1DMPE C18 4 0 14.0270; qtot: 19 LP2 1DMPE C19 5 0 14.0270; qtot: 20 LP2 1DMPE C20 6 0 14.0270; qtot: 21 LP2 1DMPE C21 7 0 14.0270; qtot: 22 LP2 1DMPE C22 8 0 14.0270; qtot: 23 LP2 1DMPE C23 9 0 14.0270; qtot: 24 LP2 1DMPE C24 10 0 14.0270; qtot: 25 LP2 1DMPE C25 11 0 14.0270; qtot: 26 LP2 1DMPE C26 12 0 14.0270; qtot: 27 LP2 1DMPE C27 13 0 14.0270; qtot: 28 LP2 1DMPE C28 14 0 14.0270; qtot: 29 LP3 1DMPE C29 15 0 15.0350; qtot: 30 LC2 1DMPE C32 16 0.50 14.0270; qtot: 31 LOS 1DMPE O33 16 -0.70 15.9994; qtot: 32 LC 1DMPE C34 16 0.80 12.0110; qtot: 33 LO 1DMPE O35 16 -0.60 15.9994; qtot: 34 LP2 1DMPE C36 17 0 14.0270; qtot: 35 LP2 1DMPE C37 18 0 14.0270; qtot: 36 LP2 1DMPE C38 19 0 14.0270; qtot: 37 LP2 1DMPE C39 20 0 14.0270; qtot: 38 LP2 1DMPE C40 21 0 14.0270; qtot: 39 LP2 1DMPE C41 22 0 14.0270; qtot: 40 LP2 1DMPE C42 23 0 14.0270; qtot: 41 LP2 1DMPE C43 24 0 14.0270; qtot: 42 LP2 1DMPE C44 25 0 14.0270; qtot: 43 LP2 1DMPE C45 26 0 14.0270; qtot: 44 LP2 1DMPE C46 27 0 14.0270; qtot: 45 LP2 1DMPE C47 28 0 14.0270; qtot: 46 LP3 1DMPE C48 29 0 15.0350; tail: [ bonds ] ; aiaj funct 1 4 1 0.1E+00 0.37450E+06 2 4 1 0.1E+00 0.37450E+06 3 4 1 0.1E+00 0.37450E+06 4 5 1 0.14700E+00 0.37660E+06 5 6 1 0.15300E+00 0.33470E+06 6 7 1
[gmx-users] Lennard Jones Parameters for Ammonia in ffoplsaa
I looked through the ffoplsaanb.itp file and see that all the H atoms except for the following four have zero LJ parameters: HC OPLS_140 alkane H HA OPLS_146 Benzene H H4 OPLS_345 Cytosine H-C6 H5 OPLS_355 Adenine Guanine H-C2 However, in the paper Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids, it states: The original OPLS (optimized potentials for liquid simulations) potential functions used a partially united-atom (UA) model; sites for nonbonded interactions are placed on all nonhydrogen atoms and on hydrogens attached to heteroatoms or carbons in aromatic rings. Later, the paper indicates that the paramters were adopted as much as possible from the OPLS-UA force field. Thus, since sites for nonbonded interactions are placed on hydrogens attached to heteroatoms , it appears to me that a site for a non-bonded interaction should exist on the H atoms within ammonia. Is my interpretation incorrect? Thanks. Darrell Date: Mon, 19 Oct 2009 19:07:22 +1100 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] Lennard Jones Parameters for Ammonia in ffoplsaa To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4adc1e3a.8010...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed Darrell Koskinen wrote: Hi, I see that the Lennard Jones parameters for the N H atoms in ammonia, represented by opls_127 and opls_128 in the file ffoplsaanb.itp are: opls_127 NT 7 14.00670-1.020 A3.42000e-01 7.11280e-01 opls_128 H 1 1.00800 0.340 A0.0e+00 0.0e+00 Why are sigma and epsilon both zero for H? Are the LJ parameters for H embedded in the parameter for NT? If so, how were these parameters combined? What do other H have? What do the OPLS-AA paper(s) have to say about such H atoms? Mark ___ 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] Lennard Jones Parameters for Ammonia in ffoplsaa
Darrell Koskinen wrote: I looked through the ffoplsaanb.itp file and see that all the H atoms except for the following four have zero LJ parameters: HC OPLS_140 alkane H HA OPLS_146 Benzene H H4 OPLS_345 Cytosine H-C6 H5 OPLS_355 Adenine Guanine H-C2 However, in the paper Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids, it states: The original OPLS (optimized potentials for liquid simulations) potential functions used a partially united-atom (UA) model; sites for nonbonded interactions are placed on all nonhydrogen atoms and on hydrogens attached to heteroatoms or carbons in aromatic rings. Later, the paper indicates that the paramters were adopted as much as possible from the OPLS-UA force field. Thus, since sites for nonbonded interactions are placed on hydrogens attached to heteroatoms , it appears to me that a site for a non-bonded interaction should exist on the H atoms within ammonia. Is my interpretation incorrect? I don't think so. Each of the above examples you've cited above is for a C-H bond in an aromatic ring. In OPLS, all N-H bonds involved hydrogen atoms with zero LJ parameters. See, for example, any backbone NH, amide (ASN/GLN), or amine (LYS/LYSH), etc and you will see the atom types used. -Justin Thanks. Darrell Date: Mon, 19 Oct 2009 19:07:22 +1100 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] Lennard Jones Parameters for Ammonia in ffoplsaa To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4adc1e3a.8010...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed Darrell Koskinen wrote: Hi, I see that the Lennard Jones parameters for the N H atoms in ammonia, represented by opls_127 and opls_128 in the file ffoplsaanb.itp are: opls_127 NT 7 14.00670-1.020 A3.42000e-01 7.11280e-01 opls_128 H 1 1.00800 0.340 A0.0e+00 0.0e+00 Why are sigma and epsilon both zero for H? Are the LJ parameters for H embedded in the parameter for NT? If so, how were these parameters combined? What do other H have? What do the OPLS-AA paper(s) have to say about such H atoms? Mark ___ 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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/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] Creating topology for a small organic molecule
Hi. I need to create a topology file for a small organic molecule that is to interact non- covalently with a DNA duplex. I want to use the amber99 force field. I saw on this mailing list that you can use acpypi with antichamber to create a topology for amber force fields. I got the amber10 tools and installed but I couldn't find any more information on how to get the antichamber package to work. I am finding this all very complicated since I am not an expert in the unix language, so if anyone knows about a good beginners tutorial on how to install antichamber and acpypi could you please let me know were to find it. Another question is, how difficult is it to create the topology for the molecule by hand for the amber99 force field. Could someone please get me started on that, if it would be easier. The molecule is a derivative of cytosine. I am using GROMACS 4 on Mac OS 10.5 Thanks. ___ 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] Lennard Jones Parameters for Ammonia in ffoplsaa
Justin A. Lemkul wrote: Darrell Koskinen wrote: I looked through the ffoplsaanb.itp file and see that all the H atoms except for the following four have zero LJ parameters: HC OPLS_140 alkane H HA OPLS_146 Benzene H H4 OPLS_345 Cytosine H-C6 H5 OPLS_355 Adenine Guanine H-C2 However, in the paper Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids, it states: The original OPLS (optimized potentials for liquid simulations) potential functions used a partially united-atom (UA) model; sites for nonbonded interactions are placed on all nonhydrogen atoms and on hydrogens attached to heteroatoms or carbons in aromatic rings. Later, the paper indicates that the paramters were adopted as much as possible from the OPLS-UA force field. Thus, since sites for nonbonded interactions are placed on hydrogens attached to heteroatoms , it appears to me that a site for a non-bonded interaction should exist on the H atoms within ammonia. Is my interpretation incorrect? I don't think so. Each of the above examples you've cited above is for a C-H bond in an aromatic ring. In OPLS, all N-H bonds involved hydrogen atoms with zero LJ parameters. See, for example, any backbone NH, amide (ASN/GLN), or amine (LYS/LYSH), etc and you will see the atom types used. I think you're both partly wrong. Type 140 is not for C-H in an aromatic ring, and if you grep 1.008 ffoplsaanb.itp you get many more H atom types with LJ. Certainly Justin's right inasmuch as amide N-H type 241 has no H LJ parameters. Perhaps there's other text that Darrell hasn't found yet, or backbone nitrogen is not considered a heteroatom :-). Mark Darrell Date: Mon, 19 Oct 2009 19:07:22 +1100 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] Lennard Jones Parameters for Ammonia in ffoplsaa To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4adc1e3a.8010...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed Darrell Koskinen wrote: Hi, I see that the Lennard Jones parameters for the N H atoms in ammonia, represented by opls_127 and opls_128 in the file ffoplsaanb.itp are: opls_127 NT 7 14.00670-1.020 A3.42000e-01 7.11280e-01 opls_128 H 1 1.00800 0.340 A0.0e+00 0.0e+00 Why are sigma and epsilon both zero for H? Are the LJ parameters for H embedded in the parameter for NT? If so, how were these parameters combined? What do other H have? What do the OPLS-AA paper(s) have to say about such H atoms? Mark ___ 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 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] Creating topology for a small organic molecule
Gunnar Widtfeldt Reginsson wrote: Hi. I need to create a topology file for a small organic molecule that is to interact non- covalently with a DNA duplex. I want to use the amber99 force field. I saw on this mailing list that you can use acpypi with antichamber to create a topology for amber force fields. I got the amber10 tools and installed but I couldn't find any more information on how to get the antichamber package to work. I am finding this all very complicated since I am not an expert in the unix language, so if anyone knows about a good beginners tutorial on how to install antichamber and acpypi could you please let me know were to find it. Since antechamber is part of the AMBER package, I would suggest reading the AMBER manual. The acpypi documentation is online: http://code.google.com/p/acpypi/ Another question is, how difficult is it to create the topology for the molecule by hand for the amber99 force field. Could someone please get me started on that, if it would be easier. The molecule is a derivative of cytosine. Parameterization is an expert topic. Please see here: http://www.gromacs.org/Documentation/How-tos/Parameterization -Justin I am using GROMACS 4 on Mac OS 10.5 Thanks. ___ 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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/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] Creating topology for a small organic molecule
Gunnar Widtfeldt Reginsson wrote: Hi. I need to create a topology file for a small organic molecule that is to interact non- covalently with a DNA duplex. I want to use the amber99 force field. I saw on this mailing list that you can use acpypi with antichamber to create a topology for amber force fields. I got the amber10 tools and installed but I couldn't find any more information on how to get the antichamber package to work. I am finding this all very complicated since I am not an expert in the unix language, so if anyone knows about a good beginners tutorial on how to install antichamber and acpypi could you please let me know were to find it. http://www.google.com.au/search?q=+antechamber+tutorial Note spelling of antechamber. Another question is, how difficult is it to create the topology for the molecule by hand for the amber99 force field. Could someone please get me started on that, if it would be easier. The molecule is a derivative of cytosine. Non-experts should use antechamber (and most experts too!) Mark I am using GROMACS 4 on Mac OS 10.5 Thanks. ___ 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 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] semiisotropic pressure coupling
Hello gmx-users, I am running an NPT simulation with 100 molecules of n-alkane and trying to impose uni-axial pressure of these molecules using semiisotropic option in grompp.mdp. However, as the box seems to distort significantly due to the imposed pressure which leads to the following error message: --- Program mdrun, VERSION 4.0.5 Source code file: ns.c, line: 2295 Fatal error: One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than the cut-off. --- I tried all vdwtype options to see whether this would mitigate the issues but was unsuccessful. is there any other options in gromacs that I can use to impose uniaxial stress? Or does anyone had any similar problems related to semi-isotropic pressure coupling? Thank you in advance. This is my grompp.mdp file configuration: integrator = md dt = 0.001 ; ps ! nsteps = 100 ; nstcomm = 1 nstxout = 250 ; collect data every 0.5 ps nstvout = 1000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype= PME rcoulomb= 0.9 vdwtype = switch rvdw= 0.7 rvdw_switch = 0.0 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; temperature coupling is on Tcoupl = v-rescale ; Groups to couple separately tc-grps = System ; Time constant (ps) and reference temperature (K) tau_t= 0.1 ref_t= 300 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 173529 constraints = all-bonds ; pressure coupling is on pcoupl = parrinello-rahman pcoupltype = semiisotropic tau_p = 0.5 compressibility = 7.10e-5 7.10e-5 ;x/y-direction, z-direction ref_p = 1.0 1000.0 ;x/y-direction, z-direction -- Yongchul Greg Chung Graduate Student Dept. of Chemical Engineering, Case Western Reserve University ___ 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] Re: Creating topology for a small organic molecule
Another question is, how difficult is it to create the topology for the molecule by hand for the amber99 force field. Could someone please get me started on that, if it would be easier. The molecule is a derivative of cytosine. I am using GROMACS 4 on Mac OS 10.5 Hi, I would advise to start with X2TOP and CHAPTER 5 of the manual. Vitaly -- Vitaly V. Chaban, Ph.D. School of Chemistry V.N. Karazin Kharkiv National University Svoboda sq.,4, Kharkiv 61077, Ukraine email: cha...@univer.kharkov.ua,vvcha...@gmail.com skype: vvchaban, cell.: +38-097-8259698 http://www-rmn.univer.kharkov.ua/chaban.html === !!! Looking for a postdoctoral position !!! === ___ 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] semiisotropic pressure coupling
Yongchul Chung wrote: Hello gmx-users, I am running an NPT simulation with 100 molecules of n-alkane and trying to impose uni-axial pressure of these molecules using semiisotropic option in grompp.mdp. However, as the box seems to distort significantly due to the imposed pressure which leads to the following error message: --- Program mdrun, VERSION 4.0.5 Source code file: ns.c, line: 2295 Fatal error: One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than the cut-off. --- You're imposing 1000 bar of pressure along the z-axis. Surely you should expect distortion? You should do some maths and work out the expected density of the box under such pressure. You still need a box large enough that the maximum cut-off length can be satisfied, so that sets the minimum number of molecules you need, and thus the initial size of the box. I tried all vdwtype options to see whether this would mitigate the issues but was unsuccessful. Don't fool with .mdp settings hoping it'll magically work. Read how they work, and you might have understood why the minimum image convention requires that the condition that provoked the above error does not arise. Mark is there any other options in gromacs that I can use to impose uniaxial stress? Or does anyone had any similar problems related to semi-isotropic pressure coupling? Thank you in advance. This is my grompp.mdp file configuration: integrator = md dt = 0.001 ; ps ! nsteps = 100 ; nstcomm = 1 nstxout = 250 ; collect data every 0.5 ps nstvout = 1000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype= PME rcoulomb= 0.9 vdwtype = switch rvdw= 0.7 rvdw_switch = 0.0 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; temperature coupling is on Tcoupl = v-rescale ; Groups to couple separately tc-grps = System ; Time constant (ps) and reference temperature (K) tau_t= 0.1 ref_t= 300 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 173529 constraints = all-bonds ; pressure coupling is on pcoupl = parrinello-rahman pcoupltype = semiisotropic tau_p = 0.5 compressibility = 7.10e-5 7.10e-5 ;x/y-direction, z-direction ref_p = 1.0 1000.0 ;x/y-direction, z-direction -- Yongchul Greg Chung Graduate Student Dept. of Chemical Engineering, Case Western Reserve University ___ 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 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] minimization problem
Hello, I merged two simulation boxes, and now I want to perform a minimization to remove the problems at their boundary! I have reduced the dt to 0.1 and emstep to 0.1 as well. But still I get the message Reading file Ih0001_81_93_204_min.tpr, VERSION 4.0.5 (double precision) Making 1D domain decomposition 8 x 1 x 1 Steepest Descents: Tolerance (Fmax) = 1.0e-05 Number of steps=705032704 t = 0.000 ps: Water molecule starting at atom 190501 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates --- Program mdrun_d_mpi, VERSION 4.0.5 Source code file: pme.c, line: 518 Fatal error: 3 particles communicated to PME node 7 are more than a cell length out of the domain decomposition cell of their charge group as part of my error message. Should I still reduce the mentioned parameters? Regards, Payman ___ 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] minimization problem
I am not sure what you refer to as dt, as there no meaning to time in EM. Anyway, I think the easiest way is to remove this ware molecule. Best, Itamar. On 26/10/2009, at 10:31 AM, Paymon Pirzadeh wrote: Hello, I merged two simulation boxes, and now I want to perform a minimization to remove the problems at their boundary! I have reduced the dt to 0.1 and emstep to 0.1 as well. But still I get the message Reading file Ih0001_81_93_204_min.tpr, VERSION 4.0.5 (double precision) Making 1D domain decomposition 8 x 1 x 1 Steepest Descents: Tolerance (Fmax) = 1.0e-05 Number of steps=705032704 t = 0.000 ps: Water molecule starting at atom 190501 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates --- Program mdrun_d_mpi, VERSION 4.0.5 Source code file: pme.c, line: 518 Fatal error: 3 particles communicated to PME node 7 are more than a cell length out of the domain decomposition cell of their charge group as part of my error message. Should I still reduce the mentioned parameters? Regards, Payman ___ 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 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] minimization problem
Sorry, That was a big typo(a mis-pasted line)! What is the suggestion anyway about emstep? Payman On Mon, 2009-10-26 at 10:43 +1100, Itamar Kass wrote: I am not sure what you refer to as dt, as there no meaning to time in EM. Anyway, I think the easiest way is to remove this ware molecule. Best, Itamar. On 26/10/2009, at 10:31 AM, Paymon Pirzadeh wrote: Hello, I merged two simulation boxes, and now I want to perform a minimization to remove the problems at their boundary! I have reduced the dt to 0.1 and emstep to 0.1 as well. But still I get the message Reading file Ih0001_81_93_204_min.tpr, VERSION 4.0.5 (double precision) Making 1D domain decomposition 8 x 1 x 1 Steepest Descents: Tolerance (Fmax) = 1.0e-05 Number of steps=705032704 t = 0.000 ps: Water molecule starting at atom 190501 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates --- Program mdrun_d_mpi, VERSION 4.0.5 Source code file: pme.c, line: 518 Fatal error: 3 particles communicated to PME node 7 are more than a cell length out of the domain decomposition cell of their charge group as part of my error message. Should I still reduce the mentioned parameters? Regards, Payman ___ 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 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 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] minimization problem
I think it is too small. Try removing the water molecule and repeat the EM. You might need to remove some molecules before you can minimise your system. Itamar On 26/10/2009, at 10:48 AM, Paymon Pirzadeh wrote: Sorry, That was a big typo(a mis-pasted line)! What is the suggestion anyway about emstep? Payman On Mon, 2009-10-26 at 10:43 +1100, Itamar Kass wrote: I am not sure what you refer to as dt, as there no meaning to time in EM. Anyway, I think the easiest way is to remove this ware molecule. Best, Itamar. On 26/10/2009, at 10:31 AM, Paymon Pirzadeh wrote: Hello, I merged two simulation boxes, and now I want to perform a minimization to remove the problems at their boundary! I have reduced the dt to 0.1 and emstep to 0.1 as well. But still I get the message Reading file Ih0001_81_93_204_min.tpr, VERSION 4.0.5 (double precision) Making 1D domain decomposition 8 x 1 x 1 Steepest Descents: Tolerance (Fmax) = 1.0e-05 Number of steps=705032704 t = 0.000 ps: Water molecule starting at atom 190501 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates --- Program mdrun_d_mpi, VERSION 4.0.5 Source code file: pme.c, line: 518 Fatal error: 3 particles communicated to PME node 7 are more than a cell length out of the domain decomposition cell of their charge group as part of my error message. Should I still reduce the mentioned parameters? Regards, Payman ___ 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 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 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 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] semiisotropic pressure coupling
On Sun, Oct 25, 2009 at 6:28 PM, Mark Abraham mark.abra...@anu.edu.auwrote: Yongchul Chung wrote: Hello gmx-users, I am running an NPT simulation with 100 molecules of n-alkane and trying to impose uni-axial pressure of these molecules using semiisotropic option in grompp.mdp. However, as the box seems to distort significantly due to the imposed pressure which leads to the following error message: --- Program mdrun, VERSION 4.0.5 Source code file: ns.c, line: 2295 Fatal error: One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than the cut-off. --- You're imposing 1000 bar of pressure along the z-axis. Surely you should expect distortion? You should do some maths and work out the expected density of the box under such pressure. You still need a box large enough that the maximum cut-off length can be satisfied, so that sets the minimum number of molecules you need, and thus the initial size of the box. Thanks for the input. I should do this. I tried all vdwtype options to see whether this would mitigate the issues but was unsuccessful. Don't fool with .mdp settings hoping it'll magically work. Read how they work, and you might have understood why the minimum image convention requires that the condition that provoked the above error does not arise. Mark is there any other options in gromacs that I can use to impose uniaxial stress? Or does anyone had any similar problems related to semi-isotropic pressure coupling? Thank you in advance. This is my grompp.mdp file configuration: integrator = md dt = 0.001 ; ps ! nsteps = 100 ; nstcomm = 1 nstxout = 250 ; collect data every 0.5 ps nstvout = 1000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype= PME rcoulomb= 0.9 vdwtype = switch rvdw= 0.7 rvdw_switch = 0.0 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; temperature coupling is on Tcoupl = v-rescale ; Groups to couple separately tc-grps = System ; Time constant (ps) and reference temperature (K) tau_t= 0.1 ref_t= 300 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 173529 constraints = all-bonds ; pressure coupling is on pcoupl = parrinello-rahman pcoupltype = semiisotropic tau_p = 0.5 compressibility = 7.10e-5 7.10e-5 ;x/y-direction, z-direction ref_p = 1.0 1000.0 ;x/y-direction, z-direction -- Yongchul Greg Chung Graduate Student Dept. of Chemical Engineering, Case Western Reserve University ___ 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 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 -- Yongchul Greg Chung Graduate Student Dept. of Chemical Engineering, Case Western Reserve University ___ 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] Re: minimization problem
Paymon Pirzadeh wrote: Hello, I merged two simulation boxes, and now I want to perform a minimization to remove the problems at their boundary! I have reduced the dt to 0.1 and emstep to 0.1 as well. But still I get the message Reading file Ih0001_81_93_204_min.tpr, VERSION 4.0.5 (double precision) Making 1D domain decomposition 8 x 1 x 1 Steepest Descents: Tolerance (Fmax) = 1.0e-05 Number of steps=705032704 t = 0.000 ps: Water molecule starting at atom 190501 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates --- Program mdrun_d_mpi, VERSION 4.0.5 Source code file: pme.c, line: 518 Fatal error: 3 particles communicated to PME node 7 are more than a cell length out of the domain decomposition cell of their charge group as part of my error message. Should I still reduce the mentioned parameters? Please see here: http://www.gromacs.org/Documentation/Errors#X_particles_communicated_to_PME_node_Y_are_more_than_a_cell_length_out_of_the_domain.0adecomposition_cell_of_their_charge_group If energy minimization is failing at step 0, there is probably some unresolvable geometry that is stopping the process. Evaluate how you built the system, and see what might be causing large forces. -Justin Regards, Payman -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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/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] minimization problem
Paymon Pirzadeh wrote: Hello, I merged two simulation boxes, Are you sure your error is not here? Inspect your result visually! :-) All the atoms need to be inside the box and non-overlapping. Mark and now I want to perform a minimization to remove the problems at their boundary! I have reduced the dt to 0.1 and emstep to 0.1 as well. But still I get the message Reading file Ih0001_81_93_204_min.tpr, VERSION 4.0.5 (double precision) Making 1D domain decomposition 8 x 1 x 1 Steepest Descents: Tolerance (Fmax) = 1.0e-05 Number of steps=705032704 t = 0.000 ps: Water molecule starting at atom 190501 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates --- Program mdrun_d_mpi, VERSION 4.0.5 Source code file: pme.c, line: 518 Fatal error: 3 particles communicated to PME node 7 are more than a cell length out of the domain decomposition cell of their charge group as part of my error message. Should I still reduce the mentioned parameters? Regards, Payman ___ 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 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] semiisotropic pressure coupling
On Sun, Oct 25, 2009 at 6:38 PM, Justin A. Lemkul jalem...@vt.edu wrote: Yongchul Chung wrote: Hello gmx-users, I am running an NPT simulation with 100 molecules of n-alkane and trying to impose uni-axial pressure of these molecules using semiisotropic option in grompp.mdp. However, as the box seems to distort significantly due to the imposed pressure which leads to the following error message: --- Program mdrun, VERSION 4.0.5 Source code file: ns.c, line: 2295 Fatal error: One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than the cut-off. --- I tried all vdwtype options to see whether this would mitigate the issues but was unsuccessful. is there any other options in gromacs that I can use to impose uniaxial stress? Or does anyone had any similar problems related to semi-isotropic pressure coupling? Thank you in advance. It seems to me that your system is simply too small to perform this kind of operation. By applying 1000 bar of pressure to such a small system, you can certainly expect the box size to deform and get smaller. Perhaps a larger number of molecules (and thus a larger box) will give you a reasonably-sized box once the 1000 bar of pressure has been applied and the system equilibrated. Yes I think I should increase my simulation size as pointed out by Mark. Also note that haphazardly changing the vdwtype or rvdw can have negative impacts on your simulation, depending on your chosen force field's sensitivity to these parameters. Thank you for pointing this out. I am relatively new to this method so am taking figure out as I go approach. -Justin This is my grompp.mdp file configuration: integrator = md dt = 0.001 ; ps ! nsteps = 100 ; nstcomm = 1 nstxout = 250 ; collect data every 0.5 ps nstvout = 1000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype= PME rcoulomb= 0.9 vdwtype = switch rvdw= 0.7 rvdw_switch = 0.0 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; temperature coupling is on Tcoupl = v-rescale ; Groups to couple separately tc-grps = System ; Time constant (ps) and reference temperature (K) tau_t= 0.1 ref_t= 300 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 173529 constraints = all-bonds ; pressure coupling is on pcoupl = parrinello-rahman pcoupltype = semiisotropic tau_p = 0.5 compressibility = 7.10e-5 7.10e-5 ;x/y-direction, z-direction ref_p = 1.0 1000.0 ;x/y-direction, z-direction -- Yongchul Greg Chung Graduate Student Dept. of Chemical Engineering, Case Western Reserve University ___ 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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/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 -- Yongchul Greg Chung Graduate Student Dept. of Chemical Engineering, Case Western Reserve University ___ 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] Re: Re: Re: Re: Does GMX compute coulomb interaction between oxygen and hydrogen in SPC water model?
Hi Thank you for your advice and sorry for disturbing you agian. I read the cooresponding relevant manual sections, I've known how to get the parameters of the tabulated funcionns. But how much is the difference between the direct computation and the table lookup method is? For example, I simulated a box of water. The results of tabluted and simple cut-off method of coulomb interation differ a lot. And is it right to use simple cut-off coulobm fuction conjunction with the PME method to get the whole coulomb contribution? 2009-10-26 Ji Xu The State Key Laboratory of Multiphase Complex System Institute of Process Engineering Chinese Academy of Sciences Beijing 100190, China Tel.: +86 10 8262 3713-804 ___ 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] Re: Re: Re: Re: Does GMX compute coulomb interaction between oxygen and hydrogen in SPC water model?
xuji wrote: Hi Thank you for your advice and sorry for disturbing you agian. I read the cooresponding relevant manual sections, I've known how to get the parameters of the tabulated funcionns. But how much is the difference between the direct computation and the table lookup method is? For example, I simulated a box of water. The results of tabluted and simple cut-off method of coulomb interation differ a lot. ... then the function in the table was not 1/r if the cut-offs were the same, or your comparison metrics were not valid, or your simulations were not equilibrated, or if equilibrated they were too short. And is it right to use simple cut-off coulobm fuction conjunction with the PME method to get the whole coulomb contribution? You can't use simple cut-off with PME, because the latter modifies the short-range interactions, as you can see in manual 4.9. If you choose PME, you will transparently use tables that look up the modified interactions, because these are faster. It's very easy to construct (garbage in = garbage out) systems in computational chemistry. Read first! Mark 2009-10-26 Ji Xu The State Key Laboratory of Multiphase Complex System Institute of Process Engineering Chinese Academy of Sciences Beijing 100190, China Tel.: +86 10 8262 3713-804 ___ 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 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] semiisotropic pressure coupling
Yongchul Chung wrote: Also note that haphazardly changing the vdwtype or rvdw can have negative impacts on your simulation, depending on your chosen force field's sensitivity to these parameters. Thank you for pointing this out. I am relatively new to this method so am taking figure out as I go approach. Well, if something works doesn't mean it's right. I would recommend doing some textbook reading, and the primary literature for the force field you've chosen. It will save you a lot of time in the long run. Remember that when publishing, you may have to defend any or all of your chosen parameters. With the right background work, you won't have to improvise these choices and face unnecessary criticism :) -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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/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
