Re: [gmx-users] pdb2gmx error with addition of terminal group
On 7/8/15 6:39 AM, anu chandra wrote: Dear Gromacs users, I am trying to use pdb2gmx tool to generate topology for my membrane protein system with chamrm36 force field. I have downloaded Gromacs compatible Chamrmm36ff from http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs. I build the N-terminal acetyl (ACE) and C-terminal N-methyl amide (NMA) group attached to the respective terminals. As shown below, I have named the residue/atom names according to the one present in 'merged.rtp' in the charmm36ff file. *** ATOM 1 CH3 ACE 1 37.718 66.293 67.509 1.00 0.00 PROA ATOM 2 HH31 ACE 1 36.850 66.906 67.178 1.00 0.00 PROA ATOM 3 HH32 ACE 1 37.393 65.240 67.617 1.00 0.00 PROA ATOM 4 HH33 ACE 1 38.522 66.381 66.751 1.00 0.00 PROA ATOM 5 C ACE 1 38.195 66.802 68.805 1.00 0.00 PROA ATOM 6 O ACE 1 37.657 67.757 69.352 1.00 0.00 PROA ATOM 7 N VAL 1 39.245 66.166 69.366 1.00 0.00 PROA ATOM 8 HN VAL 1 39.698 65.409 68.911 1.00 0.00 PROA ATOM 9 CA VAL 1 39.818 66.600 70.628 1.00 0.00 PROA ATOM 10 HA VAL 1 39.044 66.557 71.385 1.00 0.00 PROA ATOM 2599 HG1 SER 165 47.684 67.280 81.712 1.00 0.00 PROA ATOM 2600 C SER 165 46.288 64.682 84.443 1.00 0.02 PROA ATOM 2601 O SER 165 46.621 64.090 85.417 1.00 0.04 PROA ATOM 2602 N NMA 166 45.020 64.893 84.635 1.00 0.03 PROA ATOM 2603 HN NMA 166 44.986 65.779 85.049 1.00 0.00 PROA ATOM 2604 CH3 NMA 166 44.322 63.814 85.342 1.00 0.04 PROA ATOM 2605 HH31 NMA 166 44.694 62.798 85.066 1.00 0.04 PROA ATOM 2606 HH32 NMA 166 43.284 63.888 85.004 1.00 0.04 PROA ATOM 2607 HH33 NMA 166 44.382 63.845 86.467 1.00 0.06 PROA *** But, when running ' gmx pdb2gmx -f input.pdb -ter' and opting 'none' for the terminal, the pogram terminate with following error *** Back Off! I just backed up topol.top to ./#topol.top# Processing chain 1 (2607 atoms, 167 residues) Identified residue ACE1 as a starting terminus. Warning: Residue NMA166 in chain has different type (Other) from starting residue ACE1 (Protein). Identified residue SER165 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS64 CYS72 CYS95 MET100 CYS101 SG1007 SG1123 SG1473 SD1554 SG1568 CYS72 SG1123 0.857 CYS95 SG1473 2.147 1.806 MET100 SD1554 2.390 1.830 0.806 CYS101 SG1568 1.896 1.488 0.334 0.773 MET143 SD2232 1.844 1.750 1.858 2.389 1.687 Select start terminus type for ACE-1 0: NH3+ 1: NH2 2: 5TER 3: None 3 Start terminus ACE-1: None Select end terminus type for SER-165 0: COO- 1: COOH 2: CT2 3: 3TER 4: None 4 End terminus SER-165: None --- Program gmx, VERSION 5.0.4 Source code file: /usr/local/gromacs-5.0.4/src/gromacs/gmxpreprocess/pdb2top.cpp, line: 1091 Fatal error: *There is a dangling bond at at least one of the terminal ends. Fix your coordinate file, add a new terminal database entry (.tdb), or select the proper existing terminal entry.* For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- ** Can anybody help me to figure out what is wrong with my input pdb file? Note that pdb2gmx finds Ser instead of NMA as the last residue. The clue is: Warning: Residue NMA166 in chain has different type (Other) from starting residue ACE1 (Protein) You need to add NMA as Protein in residuetypes.dat. You don't want a non-patched terminus on Ser, you want a non-patched terminus on NMA. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't
[gmx-users] color map
hello all I want to build a mean smallest distance map by gromacs, but i do not know which command could make black and write picture to color picture, should anyone help me? -- Yipeng Cao Ph.D. Institute of Physics, Nankai University Tianjin China -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Problem in equilibration of POPS lipid bilayer
Hello all, I have generated a mixed lipid bilayer constituting POPS and POPC lipid molecules. I am trying to perform MD simulation but the POPS lipid molecules are tearing apart on energy minimization. Please help me..!! Thanks With regards, Padmani -- -- 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] Problem in equilibration of POPS lipid bilayer
On 7/8/15 7:57 AM, Padmani Sandhu wrote: Hello all, I have generated a mixed lipid bilayer constituting POPS and POPC lipid molecules. I am trying to perform MD simulation but the POPS lipid molecules are tearing apart on energy minimization. So either your coordinates are bad, the topology has a problem, your .mdp settings are wrong, or whatever means you've prepared the system is inadequate. Unfortunately you've provided no useful information, so it's pointless to guess. Refer to http://www.gromacs.org/Documentation/Terminology/Blowing_Up -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] color map
On 7/8/15 7:24 AM, vgsplayer1 wrote: hello all I want to build a mean smallest distance map by gromacs, but i do not know which command could make black and write picture to color picture, should anyone help me? xpm2ps -rainbow -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] no GPU detected
Hi, Sounds like you've installed something with the wrong permissions, so I would remove my CUDA stuff and try installing it again. Mark On Wed, Jul 8, 2015 at 9:07 AM Albert mailmd2...@gmail.com wrote: Hi Mark: thank you for comments. I am pretty sure that the installation is correct. I found the following for mdrun: Try 'mknod --help' for more information. chown: changing group of '/dev/nvidiactl': Operation not permitted chown: changing group of '/dev/nvidia0': Operation not permitted modprobe: ERROR: Error running install command for nvidia modprobe: ERROR: could not insert 'nvidia': Operation not permitted Do you have any idea what I should do? thx a lot On 07/08/2015 08:40 AM, Mark Abraham wrote: Hi, Don't know what the problem is, but I would make sure that I've linked GROMACS to the same CUDA installation that is providing the driver. Mark -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] pdb2gmx error
If I got it right I would suggest this. Try removing parts in your overall structure. For example let's say your system has 3 components water, ATP, TPO. Try removing all but water, try pdb2gmx, all but ATP ( like a sim in vacuo ) try once again pdb2gmx. This will make the troubled part visible. As for the error message, this comes up when you are trying to simulate a molecule that is not included in the default molecule entries. So you will have to include it manually. But when you know which part produces the error then it will be much easier. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Saman Shahriyari samanshahriy...@yahoo.com Sent: Sunday, July 5, 2015 10:06 AM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] pdb2gmx error Dear Users I am trying to run pdb2gmx (in gromacs 5.0.5 and by 43a1p.ff) on o modeled structure holding ATP, water and TPO as hetero atoms. but I am faced with the following error. I checked all LUE residues (although I have got no residue with 28215089 number) and I found no missing atom N. I am really wondering what should be my next step. could you help me on this? Fatal error:Residue 28215089 named LEU of a molecule in the input file was mapped to an entry in the topology database, but the atom N used in an interaction of type improper in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. Best regardsSaman -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] pdb2gmx error with addition of terminal group
Dear Gromacs users, I am trying to use pdb2gmx tool to generate topology for my membrane protein system with chamrm36 force field. I have downloaded Gromacs compatible Chamrmm36ff from http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs. I build the N-terminal acetyl (ACE) and C-terminal N-methyl amide (NMA) group attached to the respective terminals. As shown below, I have named the residue/atom names according to the one present in 'merged.rtp' in the charmm36ff file. *** ATOM 1 CH3 ACE 1 37.718 66.293 67.509 1.00 0.00 PROA ATOM 2 HH31 ACE 1 36.850 66.906 67.178 1.00 0.00 PROA ATOM 3 HH32 ACE 1 37.393 65.240 67.617 1.00 0.00 PROA ATOM 4 HH33 ACE 1 38.522 66.381 66.751 1.00 0.00 PROA ATOM 5 C ACE 1 38.195 66.802 68.805 1.00 0.00 PROA ATOM 6 O ACE 1 37.657 67.757 69.352 1.00 0.00 PROA ATOM 7 N VAL 1 39.245 66.166 69.366 1.00 0.00 PROA ATOM 8 HN VAL 1 39.698 65.409 68.911 1.00 0.00 PROA ATOM 9 CA VAL 1 39.818 66.600 70.628 1.00 0.00 PROA ATOM 10 HA VAL 1 39.044 66.557 71.385 1.00 0.00 PROA ATOM 2599 HG1 SER 165 47.684 67.280 81.712 1.00 0.00 PROA ATOM 2600 C SER 165 46.288 64.682 84.443 1.00 0.02 PROA ATOM 2601 O SER 165 46.621 64.090 85.417 1.00 0.04 PROA ATOM 2602 N NMA 166 45.020 64.893 84.635 1.00 0.03 PROA ATOM 2603 HN NMA 166 44.986 65.779 85.049 1.00 0.00 PROA ATOM 2604 CH3 NMA 166 44.322 63.814 85.342 1.00 0.04 PROA ATOM 2605 HH31 NMA 166 44.694 62.798 85.066 1.00 0.04 PROA ATOM 2606 HH32 NMA 166 43.284 63.888 85.004 1.00 0.04 PROA ATOM 2607 HH33 NMA 166 44.382 63.845 86.467 1.00 0.06 PROA *** But, when running ' gmx pdb2gmx -f input.pdb -ter' and opting 'none' for the terminal, the pogram terminate with following error *** Back Off! I just backed up topol.top to ./#topol.top# Processing chain 1 (2607 atoms, 167 residues) Identified residue ACE1 as a starting terminus. Warning: Residue NMA166 in chain has different type (Other) from starting residue ACE1 (Protein). Identified residue SER165 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS64 CYS72 CYS95 MET100 CYS101 SG1007 SG1123 SG1473 SD1554 SG1568 CYS72 SG1123 0.857 CYS95 SG1473 2.147 1.806 MET100 SD1554 2.390 1.830 0.806 CYS101 SG1568 1.896 1.488 0.334 0.773 MET143 SD2232 1.844 1.750 1.858 2.389 1.687 Select start terminus type for ACE-1 0: NH3+ 1: NH2 2: 5TER 3: None 3 Start terminus ACE-1: None Select end terminus type for SER-165 0: COO- 1: COOH 2: CT2 3: 3TER 4: None 4 End terminus SER-165: None --- Program gmx, VERSION 5.0.4 Source code file: /usr/local/gromacs-5.0.4/src/gromacs/gmxpreprocess/pdb2top.cpp, line: 1091 Fatal error: *There is a dangling bond at at least one of the terminal ends. Fix your coordinate file, add a new terminal database entry (.tdb), or select the proper existing terminal entry.* For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- ** Can anybody help me to figure out what is wrong with my input pdb file? Many thanks in advance Anu -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Multiple output trajectories with different sampling frequencies
Dear all, I have a problem where I am interested in fast processes in one part of the system and a slow process in another, distinct part of the system. Due to disk space limitation, I would like mdrun to write (either compressed or full precision) output trajectories for different parts of the system at different output/sampling frequencies. GROMACS does not take into account distinct parameters for compressed-x-grps, right ? I mean the second nstxout-compressed and compressed-x-precision parameters are not taken into account: ; Output frequency and precision for .xtc file nstxout-compressed = 1 100 compressed-x-precision = 1000 1000 compressed-x-grps= Protein System__!Protein As a workaround I could write the whole system at low sampling rate to an uncompressed trajectory, and one part of the system could be written at high frequency to a compressed trajectory. But what if I want a trr file also for the high-frequency sampling group ? Do you know solutions better than writing the whole system to a full precision trajectory at high sampling frequency, followed by post-processing and possibly deleting the initial raw trajectory? Many thanks! Cheers, Dr. Jan-Philipp Machtens Institute of Complex Systems - Zelluläre Biophysik (ICS-4) Forschungszentrum Jülich, Germany Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- 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] pdb2gmx error with addition of terminal group
Thanks Justin. Its working fine. On Wed, Jul 8, 2015 at 12:32 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/8/15 6:39 AM, anu chandra wrote: Dear Gromacs users, I am trying to use pdb2gmx tool to generate topology for my membrane protein system with chamrm36 force field. I have downloaded Gromacs compatible Chamrmm36ff from http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs. I build the N-terminal acetyl (ACE) and C-terminal N-methyl amide (NMA) group attached to the respective terminals. As shown below, I have named the residue/atom names according to the one present in 'merged.rtp' in the charmm36ff file. *** ATOM 1 CH3 ACE 1 37.718 66.293 67.509 1.00 0.00 PROA ATOM 2 HH31 ACE 1 36.850 66.906 67.178 1.00 0.00 PROA ATOM 3 HH32 ACE 1 37.393 65.240 67.617 1.00 0.00 PROA ATOM 4 HH33 ACE 1 38.522 66.381 66.751 1.00 0.00 PROA ATOM 5 C ACE 1 38.195 66.802 68.805 1.00 0.00 PROA ATOM 6 O ACE 1 37.657 67.757 69.352 1.00 0.00 PROA ATOM 7 N VAL 1 39.245 66.166 69.366 1.00 0.00 PROA ATOM 8 HN VAL 1 39.698 65.409 68.911 1.00 0.00 PROA ATOM 9 CA VAL 1 39.818 66.600 70.628 1.00 0.00 PROA ATOM 10 HA VAL 1 39.044 66.557 71.385 1.00 0.00 PROA ATOM 2599 HG1 SER 165 47.684 67.280 81.712 1.00 0.00 PROA ATOM 2600 C SER 165 46.288 64.682 84.443 1.00 0.02 PROA ATOM 2601 O SER 165 46.621 64.090 85.417 1.00 0.04 PROA ATOM 2602 N NMA 166 45.020 64.893 84.635 1.00 0.03 PROA ATOM 2603 HN NMA 166 44.986 65.779 85.049 1.00 0.00 PROA ATOM 2604 CH3 NMA 166 44.322 63.814 85.342 1.00 0.04 PROA ATOM 2605 HH31 NMA 166 44.694 62.798 85.066 1.00 0.04 PROA ATOM 2606 HH32 NMA 166 43.284 63.888 85.004 1.00 0.04 PROA ATOM 2607 HH33 NMA 166 44.382 63.845 86.467 1.00 0.06 PROA *** But, when running ' gmx pdb2gmx -f input.pdb -ter' and opting 'none' for the terminal, the pogram terminate with following error *** Back Off! I just backed up topol.top to ./#topol.top# Processing chain 1 (2607 atoms, 167 residues) Identified residue ACE1 as a starting terminus. Warning: Residue NMA166 in chain has different type (Other) from starting residue ACE1 (Protein). Identified residue SER165 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS64 CYS72 CYS95 MET100 CYS101 SG1007 SG1123 SG1473 SD1554 SG1568 CYS72 SG1123 0.857 CYS95 SG1473 2.147 1.806 MET100 SD1554 2.390 1.830 0.806 CYS101 SG1568 1.896 1.488 0.334 0.773 MET143 SD2232 1.844 1.750 1.858 2.389 1.687 Select start terminus type for ACE-1 0: NH3+ 1: NH2 2: 5TER 3: None 3 Start terminus ACE-1: None Select end terminus type for SER-165 0: COO- 1: COOH 2: CT2 3: 3TER 4: None 4 End terminus SER-165: None --- Program gmx, VERSION 5.0.4 Source code file: /usr/local/gromacs-5.0.4/src/gromacs/gmxpreprocess/pdb2top.cpp, line: 1091 Fatal error: *There is a dangling bond at at least one of the terminal ends. Fix your coordinate file, add a new terminal database entry (.tdb), or select the proper existing terminal entry.* For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- ** Can anybody help me to figure out what is wrong with my input pdb file? Note that pdb2gmx finds Ser instead of NMA as the last residue. The clue is: Warning: Residue NMA166 in chain has different type (Other) from starting residue ACE1 (Protein) You need to add NMA as Protein in residuetypes.dat. You don't want a non-patched terminus on Ser, you want a non-patched terminus on NMA. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users
[gmx-users] Free energy change with harmonic restraints
Dear all, I am trying to measure the free energy change associated with adding/removing harmonic restraints imposed on a ligand that is attached to a protein. Is there any way to set this up? Thank you ahead of time! Natalie Nguyen -- 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] Simulating Peptides
Hi Suniba, You touch here very complicated system that requires lot of literature research first. Few hints: 1. Amyloid-Beta (AB) is intrinsically disordered protein. The PDB you point to is a nmr structure measured in some helix-inducing solvent and it does not maintain the structure in water (physiological) solution. Thus I would be reluctant to study its unfolding because it might bring little of relevance to the water solution. If You want to look at the AB free-energy landscape in water, I would suggest looking at Pande's paper first: doi:10.1016/j.bpj.2011.12.002 2. Following from the paper, in water You face all sort of sampling problems, thus You need to reach really long time scales to obtain any meaningful result. Otherwise You might be biased toward some metastable states which stability are just artifacts of poor sampling/short timescales. 3. There's no full AB plaques structure (as far as I am aware), just its hydrophobic part (vide PDB 2beg (mono), 2lmn (di) and 2lmp (tri)). You will probably find some refs in under this pdb's. Best, Mateusz On 07/08/2015 03:35 PM, su wrote: Hello I am going to simulate the Unfolding process of Amyloid beta peptide (PDB ID 1IYT) and the fibrillar structure as well, Alone and with ligands. Can anyone suggest a good tutorial or reference article for the same? For the papers that i studies, none has explained the MD process. Regards Suniba Sent from my iPhone -- Mateusz Marianski, PhD email: marian...@fhi-berlin.mpg.de phone: +49-30-8413-4849 === Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4-6 14195 Berlin, Germany === -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Simulating Peptides
Hello I am going to simulate the Unfolding process of Amyloid beta peptide (PDB ID 1IYT) and the fibrillar structure as well, Alone and with ligands. Can anyone suggest a good tutorial or reference article for the same? For the papers that i studies, none has explained the MD process. Regards Suniba Sent from my iPhone -- 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] no GPU detected
Actually, those are errors quite clearly come from _failed_ commands that are aimed at setting up and loading the GPU driver. Nothing to do with GROMACS and no, your installation does not work unless those errors are not in sync with the state of the system. So based on those errors alone, no CUDA application will work on your system (nor will nvidia-smi). I suggest you first make sure that the GPU driver works correctly. -- Szilárd On Wed, Jul 8, 2015 at 9:07 AM, Albert mailmd2...@gmail.com wrote: Hi Mark: thank you for comments. I am pretty sure that the installation is correct. I found the following for mdrun: Try 'mknod --help' for more information. chown: changing group of '/dev/nvidiactl': Operation not permitted chown: changing group of '/dev/nvidia0': Operation not permitted modprobe: ERROR: Error running install command for nvidia modprobe: ERROR: could not insert 'nvidia': Operation not permitted Do you have any idea what I should do? thx a lot On 07/08/2015 08:40 AM, Mark Abraham wrote: Hi, Don't know what the problem is, but I would make sure that I've linked GROMACS to the same CUDA installation that is providing the driver. Mark -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] no GPU detected
Thank you for kind reply. I reinstalled the driver and now Gromacs flies. ragards On 07/08/2015 04:55 PM, Szilárd Páll wrote: Actually, those are errors quite clearly come from_failed_ commands that are aimed at setting up and loading the GPU driver. Nothing to do with GROMACS and no, your installation does not work unless those errors are not in sync with the state of the system. So based on those errors alone, no CUDA application will work on your system (nor will nvidia-smi). I suggest you first make sure that the GPU driver works correctly. -- Szilárd -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] pdb2gmx error residue not found in residue topology database
Dear gmx-users, I am really new in this field of endeavour and I am trying investigate the solubility of peptides in organic solvents, I built a simple tripeptide (gly-gly-gly) using Gaussian 5.0 and I convert the output file(.out) to .pdb. I am now trying to use pdb2gmx tool to generate topology for my peptide using GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) I was promoted with an error residue not found in residue topology database” I checked GROMACS website at http://www.gromacs.org/Documentation/Errors I learned the residue must have the same name as in the force field, please I don’t know the naming convention of this force field please HELP. Thanks Ali H. Department of Chemistry University Dutse -- 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] Simulating Peptides
Thank You very much for the quick and detailed reply. I will study more according to points you mentioned and then start any fruitful simulation. Best Regards Sent from my iPhone On 08-Jul-2015, at 7:31 pm, Mateusz Marianski marian...@fhi-berlin.mpg.de wrote: Hi Suniba, You touch here very complicated system that requires lot of literature research first. Few hints: 1. Amyloid-Beta (AB) is intrinsically disordered protein. The PDB you point to is a nmr structure measured in some helix-inducing solvent and it does not maintain the structure in water (physiological) solution. Thus I would be reluctant to study its unfolding because it might bring little of relevance to the water solution. If You want to look at the AB free-energy landscape in water, I would suggest looking at Pande's paper first: doi:10.1016/j.bpj.2011.12.002 2. Following from the paper, in water You face all sort of sampling problems, thus You need to reach really long time scales to obtain any meaningful result. Otherwise You might be biased toward some metastable states which stability are just artifacts of poor sampling/short timescales. 3. There's no full AB plaques structure (as far as I am aware), just its hydrophobic part (vide PDB 2beg (mono), 2lmn (di) and 2lmp (tri)). You will probably find some refs in under this pdb's. Best, Mateusz On 07/08/2015 03:35 PM, su wrote: Hello I am going to simulate the Unfolding process of Amyloid beta peptide (PDB ID 1IYT) and the fibrillar structure as well, Alone and with ligands. Can anyone suggest a good tutorial or reference article for the same? For the papers that i studies, none has explained the MD process. Regards Suniba Sent from my iPhone -- Mateusz Marianski, PhD email: marian...@fhi-berlin.mpg.de phone: +49-30-8413-4849 === Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4-6 14195 Berlin, Germany === -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Calculating hydrogen bonding density - issues with g_sas?
Is g_sas applicable to more than one molecule at a time? I have 4500 water molecules in the liquid state. I am using the command: g_sas -f traj.trr -s topol.tpr -tv volume.xvg On Tue, Jul 7, 2015 at 10:31 AM, Dan Gil dan.gil9...@gmail.com wrote: I am using the default radius of 0.14 nm. In this case, I believe that it is consistent. Nevertheless, I have tried using a probe much larger with no significant difference in the results. The way I am using g_sas is: I have 4500 water molecules. I specified that I want the volume of all of them. On Tue, Jul 7, 2015 at 10:11 AM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, Is the radius being used consistent with your assumption? Mark On Tue, Jul 7, 2015 at 3:58 PM Dan Gil dan.gil9...@gmail.com wrote: Hi, I am using g_hbond to count the number of h-bonds and then g_sas to calculate the volume. I want to get the number of hydrogen bonds per volume. But I am having issues with g_sas - the volume calculated is about one half of the expected value. For instance, in a pure water system (NVT, SPCE, T=300K) periodic in the x and y directions, volume was found to be about 60nm^3, whereas I expected 130nm^3. I would appreciate any advice! Best, -- Dan Gil Case Western Reserve University | Class of 2016 Researcher, Department of Chemical Engineering dan.gil9...@gmail.com -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Dan Gil Case Western Reserve University | Class of 2016 Researcher, Department of Chemical Engineering dan.gil9...@gmail.com -- Dan Gil Case Western Reserve University | Class of 2016 Researcher, Department of Chemical Engineering dan.gil9...@gmail.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] pdb2gmx error residue not found in residue topology database
Look at the file: residuetypes.dat in the ../top/ directory of your installation. It lists all the residue names and more. Peter Stern Weizmann Institute Sent from my iPad On 8 ביולי 2015, at 17:45, Hamisu Aliyu Mohd hamisu.kaza...@yahoo.com wrote: Dear gmx-users, I am really new in this field of endeavour and I am trying investigate the solubility of peptides in organic solvents, I built a simple tripeptide (gly-gly-gly) using Gaussian 5.0 and I convert the output file(.out) to .pdb. I am now trying to use pdb2gmx tool to generate topology for my peptide using GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) I was promoted with an error residue not found in residue topology database” I checked GROMACS website at http://www.gromacs.org/Documentation/Errors I learned the residue must have the same name as in the force field, please I don’t know the naming convention of this force field please HELP. Thanks Ali H. Department of Chemistry University Dutse -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Problem in .gro file
Hi, I have shared the files via Dropbox https://www.dropbox.com/sh/bp3d1ugn233domy/AACSSs8fFCmXn_MBRjZBheoda?dl=0 On Wed, Jul 8, 2015 at 4:54 AM, Justin Lemkul jalem...@vt.edu wrote: On 7/7/15 9:13 AM, faride badalkhani wrote: Dear Justin, This is the link you can find the prepared files: http://www.4shared.com/zip/HpM1O820ce/FF_online.html Please use a service that isn't laden with spam links. I can't figure out what to click without poisoning my computer. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] pdb2gmx error residue not found in residue topology database
How you converted the gaussian file into .pdb? Because once i did the same and suffered from some missing co ordinates. Sent from my iPhone On 08-Jul-2015, at 11:16 pm, Peter Stern peter.st...@weizmann.ac.il wrote: Look at the file: residuetypes.dat in the ../top/ directory of your installation. It lists all the residue names and more. Peter Stern Weizmann Institute Sent from my iPad On 8 ביולי 2015, at 17:45, Hamisu Aliyu Mohd hamisu.kaza...@yahoo.com wrote: Dear gmx-users, I am really new in this field of endeavour and I am trying investigate the solubility of peptides in organic solvents, I built a simple tripeptide (gly-gly-gly) using Gaussian 5.0 and I convert the output file(.out) to .pdb. I am now trying to use pdb2gmx tool to generate topology for my peptide using GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) I was promoted with an error residue not found in residue topology database” I checked GROMACS website at http://www.gromacs.org/Documentation/Errors I learned the residue must have the same name as in the force field, please I don’t know the naming convention of this force field please HELP. Thanks Ali H. Department of Chemistry University Dutse -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Fw: Simulation of polarizable Carbon nanotubes
Hi Justin, Thank you so much for your suggestion. Before, trying to simulate polarizable CNTs using the new code based on drude oscillator, I've been trying to simulate systems of SWM4-NDP water with KCl to make myself familiarize with the new code. At first, I was incorporating drude parameters (e.g. drude=yes with SCF, NPT), but, I was getting segmentation fault. Then, I turned off the drude parameters and ran the simulation. I did not get the error. However, the system is freezing (no movement of atoms). I am assuming it's an artifact, but, I'm not sure what is the reason behind this. I simulated the similar system using older version of gromacs (4.6.1), and I did not face the issue of artifacts. Can you please provide me any solution to overcome this issue? FYI: I've been using isotropic polarizability of water and ions. Thanks in advance. I modified the .mdp file that you provided in your recent paper on drude oscillator in Gromacs. My .itp file looks like: [ defaults ] LJ Geometric [ atomtypes ] ;name mass charge ptype c6 c12 WO 15.99940 0.0 A 0.0 0.0 WH 1.00800 0.0 A 0.0 0.0 WS 0.0 0.0 S 0.0 0.0 WD 0.0 0.0 D 0.0 0.0 Kc 39.0983 0.0 A 0.0 0.0 Ks 0.000 0.0 S 0.0 0.0 CLc 35.45300 0.0 A 0.0 0.0 CLs 0.000 0.0 S 0.0 0.0 [ nonbond_params ] WO WO 1 3.67796770E-03 3.83182123E-06 WO Kc 1 2.46E-03 2.492E-06 WO CLc 1 6.69E-03 1.84E-05 Kc Kc 1 1.646E-03 1.62E-06 CLc CLc 1 12.16158E-03 8.8248256E-05 Kc CLc 1 4.474E-03 1.196E-05 [ moleculetype ] ; molname nrexcl SOL 2 [ atoms ] ; id at type res nr residu name at name cg nr charge 1 WO 1 SOL OW 1 1.71636 2 WH 1 SOL HW 1 0.55733 3 WH 1 SOL HW 1 0.55733 4 WD 1 SOL DW 1 -1.11466 5 WS 1 SOL SW 1 -1.71636 #ifdef ANISOTROPIC [ water_polarization ] ; See notes above. Alphas in nm^3 (See ref. above) ; O H H D S funct al_x al_y al_z rOH rHH rOD 1 2 3 4 5 1 0.001415 0.001528 0.001468 0.09572 0.15139 0.0137408 #else [ polarization ] ; See notes above. alpha (nm^3) 1 5 1 0.00097822 #endif [ bonds ] 1 2 1 0.09572 458148. 1 3 1 0.09572 458148. [ angles ] ; i j k 2 1 3 1 104.52 417.6 [ dummies3 ] ; Dummy from funct a b 4 1 2 3 2 0.5 0.024034 [ exclusions ] ; iatom excluded from interaction with i 1 2 3 4 5 2 1 3 4 5 3 1 2 4 5 4 1 2 3 5 5 1 2 3 4 [ moleculetype ] ; molname nrexcl K+ 1 [ atoms ] ; id at type res nr residu name at name cg nr charge 1 Kc 1 K Kc 1 2.580968 2 Ks 1 K Ks 1 -1.580968 [ polarization ] ; See notes above. alpha (nm^3) 1 2 1 0.000830 [ exclusions ] ; iatom excluded from interaction with i 1 2 2 1 [ moleculetype ] ; molname nrexcl Cl- 1 [ atoms ] ; id at type res nr residu name at name cg nr charge 1 CLc 1 CL CLc 1 2.457187 2 CLs 1 CL CLs 1 -3.457187 [ polarization ] ; See notes above. alpha (nm^3) 1 2 1 0.0003969 [ exclusions ] ; iatom excluded from interaction with i 1 2 2 1 Let me know if you require any further information. I've taken all the parameters from literature on SWM4-NDP water and monovalent ions. Regards,Golam Mortuza On Monday, June 29, 2015 11:01 AM, Justin Lemkul jalem...@vt.edu wrote: On 6/29/15 1:56 PM, S.M. Golam Mortuza wrote: Hi Justin, Thank you so much for your suggestion. Also, thanks a lot for taking a close look at the paper. I've contacted with the authors of the paper and asked the topology. In the mean time, I've tried simulating a system of a benzene using the method described in the paper, and it ran successfully. So, I am assuming it's the problem with the value of polarization for carbon nanotube. Good to hear! Anyway, I've compiled the new code as per your suggestion. I am just wondering whether it's possible to merge this new code with the previous version of gromacs, which is already installed in my computer. Or, are they two different executables and need to be run separately based on my preference? If the latter case, what is the executable names for the new code. For instance, we use grompp, mdrun, etc. for the regular version of gromacs. Are they
Re: [gmx-users] Problem in .gro file
On 7/8/15 2:00 PM, faride badalkhani wrote: Hi, I have shared the files via Dropbox https://www.dropbox.com/sh/bp3d1ugn233domy/AACSSs8fFCmXn_MBRjZBheoda?dl=0 You can't repeat atom names within a residue. This: HETATM1 CA AMC A 1 -9.327 -1.032 -2.562 C HETATM2 HC AMC A 1 -10.101 -1.364 -3.324 H HETATM3 HC AMC A 1 -8.844 -0.232 -3.007 H HETATM4 CA AMC A 1 -8.327 -2.174 -2.335 C HETATM5 HC AMC A 1 -8.850 -3.081 -2.383 H HETATM6 HC AMC A 1 -7.952 -2.132 -1.306 H HETATM7 N2 AMC A 1 -9.932 -0.563 -1.272 N HETATM8 N2 AMC A 1 -7.129 -2.164 -3.281 N gets turned into: 1AMC CA1 -0.933 -0.103 -0.256 1AMC HC2 -1.010 -0.136 -0.332 1AMC N23 -0.993 -0.056 -0.127 because pdb2gmx cleans up duplicate atoms. You went from 1124 atoms in the PDB file to 423 in the GRO file. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] no GPU detected
Hi Mark: thank you for comments. I am pretty sure that the installation is correct. I found the following for mdrun: Try 'mknod --help' for more information. chown: changing group of '/dev/nvidiactl': Operation not permitted chown: changing group of '/dev/nvidia0': Operation not permitted modprobe: ERROR: Error running install command for nvidia modprobe: ERROR: could not insert 'nvidia': Operation not permitted Do you have any idea what I should do? thx a lot On 07/08/2015 08:40 AM, Mark Abraham wrote: Hi, Don't know what the problem is, but I would make sure that I've linked GROMACS to the same CUDA installation that is providing the driver. Mark -- 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] how to make 8M solutions??
Hi, Since you know how to add n molecules, and you want a solution with a given molality, work out how many molecules that is, and then add that many molecules. Decide whether you care about the volume excluded by the protein when considering what that molality means. Mark On Wed, Jul 8, 2015 at 6:51 AM SAPNA BORAH sapnauser...@gmail.com wrote: Dear all, I am trying to add gdmcl to a protein, however I am unable to make molal solutions. I can add gdmcl by -nmol command but to make molal solutions is giving me a hard time. This is a basic query but it has been bugging me for quite a long time. Please put some light on doing this... I have been using the following commands to make the gdmcl box: editconf -f mod.pdb -bt cubic -d 0.1 -box 5 5 5 -o box.gro genbox -cp box.gro -ci file_1.pdb -p topol.top -o guan.pdb -nmol 100 editconf -f guan.pdb -bt cubic -d 1.2 -o box_2.gro genbox -cp box_2.gro -cs spc216.gro -p topol.top -o solvated.gro The simulations I have been running well with the included 100 GdmCl, however, the problem with making the molal solutions still remains. Regards, Sapna Sapna Mayuri Borah Research student Tezpur University, India -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] no GPU detected
Hi, Don't know what the problem is, but I would make sure that I've linked GROMACS to the same CUDA installation that is providing the driver. Mark On Wed, Jul 8, 2015 at 8:18 AM Albert mailmd2...@gmail.com wrote: Hello: I've got a GPU machine with 4 GPU cards. I compiled gromacs-5.0.5 with GPU support successfully, and I try to run some jobs. However, the job always failed with following messages: Command line: mdrun_mpi -s md2.tpr -g -v md.log -c md.gro -x md.xtc -e md.edr -gpu_id 01 -ntomp 12 Back Off! I just backed up md.log to ./#md.log.6# Number of hardware threads detected (48) does not match the number reported by OpenMP (24). Consider setting the launch configuration manually! NOTE: Error occurred during GPU detection: no CUDA-capable device is detected Can not use GPU acceleration, will fall back to CPU kernels. Reading file md2.tpr, VERSION 5.0.5 (single precision) Changing nstlist from 10 to 20, rlist from 1 to 1.028 Using 2 MPI processes Using 12 OpenMP threads per MPI process No GPUs detected on host cudaC I am just wondering, what's problem? I use nvidia-smi and can find the GPU without any problem. I've installed CUDA7 in the linux X64 system. thank you very much. Albert -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] no GPU detected
Hello: I've got a GPU machine with 4 GPU cards. I compiled gromacs-5.0.5 with GPU support successfully, and I try to run some jobs. However, the job always failed with following messages: Command line: mdrun_mpi -s md2.tpr -g -v md.log -c md.gro -x md.xtc -e md.edr -gpu_id 01 -ntomp 12 Back Off! I just backed up md.log to ./#md.log.6# Number of hardware threads detected (48) does not match the number reported by OpenMP (24). Consider setting the launch configuration manually! NOTE: Error occurred during GPU detection: no CUDA-capable device is detected Can not use GPU acceleration, will fall back to CPU kernels. Reading file md2.tpr, VERSION 5.0.5 (single precision) Changing nstlist from 10 to 20, rlist from 1 to 1.028 Using 2 MPI processes Using 12 OpenMP threads per MPI process No GPUs detected on host cudaC I am just wondering, what's problem? I use nvidia-smi and can find the GPU without any problem. I've installed CUDA7 in the linux X64 system. thank you very much. Albert -- 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] Fw: Simulation of polarizable Carbon nanotubes
On 7/8/15 4:57 PM, S.M. Golam Mortuza wrote: Hi Justin, Thank you so much for your suggestion. Before, trying to simulate polarizable CNTs using the new code based on drude oscillator, I've been trying to simulate systems of SWM4-NDP water with KCl to make myself familiarize with the new code. At first, I was incorporating drude parameters (e.g. drude=yes with SCF, NPT), but, I was getting segmentation fault. Then, I turned off the drude parameters and ran the simulation. I did not get the error. However, the system is freezing (no movement of atoms). I am assuming it's an artifact, but, I'm not sure what is the reason behind this. I simulated the similar system using older version of gromacs (4.6.1), and I did not face the issue of artifacts. Can you please provide me any solution to overcome this issue? FYI: I've been using isotropic polarizability of water and ions. Thanks in advance. I modified the .mdp file that you provided in your recent paper on drude oscillator in Gromacs. My .itp file looks like: [ defaults ] LJGeometric [ atomtypes ] ;namemass charge ptype c6c12 WO15.99940 0.0 A 0.00.0 WH 1.00800 0.0 A0.00.0 WS 0.0 0.0 S 0.00.0 WD 0.00.0D 0.00.0 Kc 39.09830.0 A 0.00.0 Ks0.000 0.0 S 0.00.0 CLc 35.45300 0.0 A 0.00.0 CLs0.000 0.0 S 0.00.0 [ nonbond_params ] WO WO 1 3.67796770E-03 3.83182123E-06 WO Kc 1 2.46E-03 2.492E-06 WO CLc 1 6.69E-03 1.84E-05 Kc Kc 1 1.646E-03 1.62E-06 CLc CLc 1 12.16158E-03 8.8248256E-05 Kc CLc 1 4.474E-03 1.196E-05 [ moleculetype ] ; molnamenrexcl SOL2 [ atoms ] ; idat typeres nr residu nameat namecg nrcharge 1WO1SOLOW11.71636 2WH1SOLHW10.55733 3WH1SOLHW10.55733 4WD1SOLDW1 -1.11466 5WS1SOLSW1-1.71636 #ifdef ANISOTROPIC [ water_polarization ] ; See notes above. Alphas in nm^3 (See ref. above) ; O H H D S funct al_x al_y al_z rOHrHHrOD 1 2 3 4 5 10.001415 0.001528 0.001468 0.095720.15139 0.0137408 #else [ polarization ] ; See notes above.alpha (nm^3) 151 0.00097822 #endif [ bonds ] 1 2 1 0.09572 458148. 1 3 1 0.09572 458148. [ angles ] ; i j k 2 1 31 104.52 417.6 [ dummies3 ] ; Dummy fromfunctab 4 1 2 3 2 0.5 0.024034 [ exclusions ] ; iatom excluded from interaction with i 12345 21345 31245 41235 51234 [ moleculetype ] ; molname nrexcl K+1 [ atoms ] ; idat type res nr residu name at name cg nr charge 1 Kc 1 K Kc12.580968 2 Ks 1 K Ks1 -1.580968 [ polarization ] ; See notes above. alpha (nm^3) 1 2 1 0.000830 [ exclusions ] ; iatom excluded from interaction with i 1 2 2 1 [ moleculetype ] ; molname nrexcl Cl- 1 [ atoms ] ; idat type res nr residu name at name cg nr charge 1 CLc 1 CL CLc 12.457187 2 CLs 1 CL CLs 1 -3.457187 [ polarization ] ; See notes above. alpha (nm^3) 1 2 1 0.0003969 [ exclusions ] ; iatom excluded from interaction with i 1 2 2 1 Let me know if you require any further information. I've taken all the parameters from literature on SWM4-NDP water and monovalent ions. Please send me all of the required input files off-list, along with a list of your exact sequence of commands. I'll have to run through a debugger to figure out where the seg fault is coming from. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to
Re: [gmx-users] Fw: Simulation of polarizable Carbon nanotubes
On 7/8/15 4:57 PM, S.M. Golam Mortuza wrote: This is the problem: [ bonds ] 1 2 1 0.09572 458148. 1 3 1 0.09572 458148. [ angles ] ; i j k 2 1 31 104.52 417.6 SWM4-NDP is a rigid water model. You should not be using flexible bonds and angles. Remove this section and replace with [ settles ] ; i j funct length 1 1 0.09572 0.15139 The run proceeds fine with proper rigid treatment of the water. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Problem in equilibration of POPS lipid bilayer
Thank you Justin, I was not paying attention toward the wrong .itp file. I found correct topology of POPS from the site of *Robert Vácha* ( http://lcc.ncbr.muni.cz/~robert/publikacee.htm) and now the problem is sorted. With regards, Padmani On Wed, Jul 8, 2015 at 5:29 PM, Justin Lemkul jalem...@vt.edu wrote: [image: Boxbe] https://www.boxbe.com/overview This message is eligible for Automatic Cleanup! (jalem...@vt.edu) Add cleanup rule https://www.boxbe.com/popup?url=https%3A%2F%2Fwww.boxbe.com%2Fcleanup%3Ftoken%3DmmoH72dBff9ZLiT0LvtDttmTeoAIJHUudSk%252F0Jy3Wj5PDtaYCmYNUvLiwcpVGQetXmORmmUwTKY1iZgmS3u%252BT1Cuf1zNqR0VTjA6SCIvYvhvQHqzA0fRA5DYa%252BEDp%252Bnzaw0RjafgFxM%253D%26key%3DE%252F3a6xm5v2zwgzdAiaRFYXkYDnPFgp7boBDAfYepou8%253Dtc_serial=21904080572tc_rand=1921652829utm_source=stfutm_medium=emailutm_campaign=ANNO_CLEANUP_ADDutm_content=001 | More info http://blog.boxbe.com/general/boxbe-automatic-cleanup?tc_serial=21904080572tc_rand=1921652829utm_source=stfutm_medium=emailutm_campaign=ANNO_CLEANUP_ADDutm_content=001 On 7/8/15 7:57 AM, Padmani Sandhu wrote: Hello all, I have generated a mixed lipid bilayer constituting POPS and POPC lipid molecules. I am trying to perform MD simulation but the POPS lipid molecules are tearing apart on energy minimization. So either your coordinates are bad, the topology has a problem, your .mdp settings are wrong, or whatever means you've prepared the system is inadequate. Unfortunately you've provided no useful information, so it's pointless to guess. Refer to http://www.gromacs.org/Documentation/Terminology/Blowing_Up -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- *Padmani sandhu* *Research Scholar,* *Center for Computational Biology and Bioinformatics,* *Central University of Himachal Pradesh,* *Temporary Academic Block, Shahpur * *Pin 176206, District Kangra,* *Himachal Pradesh, India* -- 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] trouble diagnosing a simulation that's blowing up (shake not converging -- segmentation fault)
Hello, I deleted the email and can't respond to my last reply directly - sorry! I got this response from Mark Abraham: Hi, Try doing some EM and initial equilibration with no constraints at all, perhaps? Mark I tried commenting out the shake commands, and got a short (5000 step) simulation to run just fine without blowing up. Before, I would get shake warnings from the first few steps and a segmentation fault around step 13 or 14. I would like to be able to simulate with rigid molecules, though. Why would the simulation work with flexible molecules but not rigid ones? Also, in the example .mdp file for tip4p water, there is the (outdated) option, 'unconstrained-start', which is now 'continuation'. I got errors when trying to make the input .tpr file when I attempted to set that option to 'yes'. The warning said it was because I want Gromacs to generate velocities to start the simulation, which is incompatible with that command. Is there another way I can try to start the simulation unconstrained? Or would you suggest another idea to fix my shake warnings? Thanks very much for your help, Nathan - Original Message - From: Nathan K Houtz nho...@purdue.edu To: gmx-us...@gromacs.org Sent: Monday, July 6, 2015 9:08:33 PM Subject: trouble diagnosing a simulation that's blowing up (shake not converging -- segmentation fault) Hello, I'm attempting to simulate ice ih in a triclinic box with a rigid tip4p water model. As the subject says, I get warnings (almost immediately) that shake failed to converge in 1000 steps and then eventually a segmentation fault. Gromacs documentation suggests that this is a result of my simulation blowing up. I tried decreasing the timestep down to 0.0001 ps, lowering the temperature, and minimizing further (down to 100 kJ/mol/nm) but nothing worked. I mostly used modified versions of the files available on this page: http://www.sklogwiki.org/SklogWiki/index.php/GROMACS_files_for_the_TIP4P/2005_model except the .gro file, which is my own. I did comment out the pressure coupling algorithms because I got a note that the barostat was unsuitable for equillibration, but I want NVT anyway. The temperature is 120.0 K and the coulomb type is PME. I've double checked and am satisfied with the interaction parameters in the topology file, so I'm out of ideas on where my mistake migh! t be. Here are the commands and files I used, in case it helps: gmx grompp -f minim.mdp -c water_5100.gro -p water_topol.top -o em.tpr gmx mdrun -v -deffnm em gmx grompp -f water_5100.mdp -c em.gro -p water_topol.top -o water.tpr gmx mdrun -deffnm water Here is the minim.mdp file: http://textuploader.com/iggv The water_topol.top file: http://textuploader.com/igpd And the water_5100.mdp file: http://textuploader.com/igzj You'll notice a slight mistake in the naming convention. There are 1700 molecules in the simulation, but everything is named something like '..._5100', even though tip4p water has a virtual site (making 4 particles). My .gro file does in fact have 6800 atoms, not 5100, I just neglected to rename the files because it's easier. Unfortunately I can't upload the .gro file because it's too big. I realize the problem could be there but I won't attach a large file unless it's specifically requested. Here's a sample: Triclinic Frozen Water Simulation 6800 1WATER OW1 0.261 0.000 0.000 0. 0. 0. 1WATER HW2 0.261 0.000 0.082 0. 0. 0. 1WATER HW3 0.343 -0.000 -0.027 0. 0. 0. 1WATER DW4 0.272 0.000 0.007 0. 0. 0. 2WATER OW5 0.261 0.000 0.736 0. 0. 0. 2WATER HW6 0.261 0.000 0.818 0. 0. 0. 2WATER HW7 0.343 0.000 0.709 0. 0. 0. 2WATER DW8 0.272 0.000 0.743 0. 0. 0. 3WATER OW9 0.261 0.000 1.472 0. 0. 0. 3WATER HW 10 0.261 0.000 1.554 0. 0. 0. 3WATER HW 11 0.343 0.000 1.445 0. 0. 0. 3WATER DW 12 0.272 0.000 1.479 0. 0. 0. 4WATER OW 13 0.261 0.000 2.208 0. 0. 0. 4WATER HW 14 0.261 0.000 2.290 0. 0. 0. 4WATER HW 15 0.343 0.000 2.181 0. 0. 0. 4WATER DW 16 0.272 0.000 2.215 0. 0. 0. 5WATER OW 17 0.261 0.000 2.944 0. 0. 0. 5WATER HW 18 0.261 0.000 3.026 0. 0. 0. 5WATER HW 19 0.343 0.000 2.917 0. 0. 0. 5WATER DW 20 0.272 0.000 2.951 0. 0. 0. 6WATER OW 21 -0.130 0.677 0.000 0. 0. 0. 6WATER HW 22 -0.130 0.677 0.082 0. 0. 0. 6WATER HW 23 -0.048 0.677 -0.027 0. 0. 0. 6WATER DW 24 -0.119 0.677
[gmx-users] How to justify when the trajectory reached equilibrium
Hi, I did a 70-ns MD simulation. I wonder how to justify when the trajectory reached equilibrium... Seen from RMSD-time curve of C-alpha, the curve reached about 1 nm at 12 ns and kept stable after that. Could I justify that the system reached equilibrium at 12 ns? Are there any methods/criteria to justify the equilibrium other than RMSD evolution? Thanks a lot, Qing -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Energy minimization
Hi, I want to do MD simulation of protein-DNA-ligand using Gromacs 5.0.4.,when I do energy minimization, my system is converged but has positive potential energy. also this step only takes 3 second! for next step (pr), gives error: your system is not equilibrated well and blowing up! I chcked my em.pdb file and I saw the Sol box is separated from protein and DNA! Could you please help me, what should I do?what part of my set is wrong? my em.mdp: define = -DFLEXIBLE integrator = cg ; steep nsteps = 4000 nstlist = 1 constraints = none emtol = 100.0 nstcgsteep = 10 ; do a steep every 10 steps of cg emstep = 0.01 ; used with steep nstcomm = 1 nstcalcenergy = 1.2 ewald_rtol = 1e-05 coulombtype = PME cutoff-scheme = Group ns_type = grid rlist = 1.4 rcoulomb =1.4 rvdw = 1.4 Tcoupl = no Pcoupl = no gen_vel = no nstxout = 0 ; write coords every # step optimize_fft = yes Sincerely, Malihe -- 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.
