Re: [gmx-users] g_wham position 0
Hi, the key Umb. Pos. 0.0 indicates the the umbrella center of this simulaiton is at 0.0, not that the profile should starts at zero. Beginning and end of profile are set with -min -max. cheers, Jochen Am 3/22/12 7:03 PM, schrieb rainy908: Hi all, I am experiencing a potential problem with my PMF curve not starting at position 0 of the reaction coordinate, which is defined by a path starting from 0.0 nm and ending at 0.5 nm. When I run the GROMACS g_wham analysis at Umb. Pos 0.0 (see below), to say, 0.02 nm, the PMF curve doesn't start out at 0.0 nm but gets offset to ~0.01 nm in the resulting figure. Its corresponding histogram also gets offset by the same amount. This is particularly peculiar to me because my frame1 *is* the structure at 0.0nm of the S path. I also double-checked my COLVAR file and there are no negative values in my COLVAR file: # UMBRELLA3.0 # Compnent selection: 0 0 1 # nSkip 1 # Ref. Group 'TestAtom' # Nr. of pull groups 1 # Group 1 'GR1' Umb. Pos. 0.0 Umb. Cons. 5 # 0.0300 0.47500 0.0400 0.000103337 0.0500 0.000163820 0.0600 0.000265547 0.0700 0.000408777 0.0800 0.000550200 0.0900 0.000653522 Has anyone else experienced this problem before? I'm hoping it's just some minor issue in g_wham. I even invoked the -zprof0 flag to - zprof 0 and it did not set my PMF curve to start at 0. Sincerely, Lili -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Phone: +49-551-39-14189 http://cmb.bio.uni-goettingen.de/ --- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Statistical error of Umbrella Sampling
Hi, check http://pubs.acs.org/doi/abs/10.1021/ct100494z and g_wham -h Cheers, Jochen Am 3/20/12 10:10 AM, schrieb Steven Neumann: Dear Gmx Users, Could you please write me how to evaluate the statistical error of the binding free energy obtained by umbrella sampling? Thank you Steven -- --- Dr. Jochen Hub Computational Molecular Biophysics Group Institute for Microbiology and Genetics Georg-August-University of Göttingen Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. Phone: +49-551-39-14189 http://cmb.bio.uni-goettingen.de/ --- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] REMD equilibration
Dear gromacs users, I have to perform REMD simulation, but since it is the first time I apply this tecnique I have a question regarding system equilibration. As far as I know, befaore starting the REMD each replica has to be equlibrated. The equilibration has to be carried out in the NPT ensemble or only in the NVT? Thanks in advance, Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] REMD equilibration
On 03/23/2012 10:41 AM, francesco oteri wrote: Dear gromacs users, I have to perform REMD simulation, but since it is the first time I apply this tecnique I have a question regarding system equilibration. As far as I know, befaore starting the REMD each replica has to be equlibrated. The equilibration has to be carried out in the NPT ensemble or only in the NVT? Depends on the ensemble you want to simulate. If the replica you are interested in should be simulated in NVT you should equilibrate this replica well and take care that all replicas have the same volume (meaning that the replicas with higher T have very high pressures). You also can simulate each replica in an NPT ensemble (and also equilibrate the replicas with NPT). When the pressure is included in the Metropolis criteria for the exchange of the trajectories. Thanks in advance, Francesco all the best Sebastian -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] REMD equilibration
Hi Francesco, It should be the same ensemble, in which you want to carry out the production REMD. Andreas From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of francesco oteri Sent: 23 March 2012 09:41 To: Discussion list for GROMACS users Subject: [gmx-users] REMD equilibration Dear gromacs users, I have to perform REMD simulation, but since it is the first time I apply this tecnique I have a question regarding system equilibration. As far as I know, befaore starting the REMD each replica has to be equlibrated. The equilibration has to be carried out in the NPT ensemble or only in the NVT? Thanks in advance, Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] REMD equilibration
I understand, I am planning to run REMD between 300 and 600 K, so I think it is better equlibrating in NVT ensemble because at high temperature water evaporates, is it? Francesco Il giorno 23 marzo 2012 10:53, Kukol, Andreas a.ku...@herts.ac.uk ha scritto: Hi Francesco, It should be the same ensemble, in which you want to carry out the production REMD. Andreas From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of francesco oteri Sent: 23 March 2012 09:41 To: Discussion list for GROMACS users Subject: [gmx-users] REMD equilibration Dear gromacs users, I have to perform REMD simulation, but since it is the first time I apply this tecnique I have a question regarding system equilibration. As far as I know, befaore starting the REMD each replica has to be equlibrated. The equilibration has to be carried out in the NPT ensemble or only in the NVT? Thanks in advance, Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] BUG: Free energy calculation
Dear gromacs users/developers, when trying to couple in a peptide into a membrane with: ; Define position restraints for peptide define = -DPOSRES ; couple in peptide free_energy = yes init_lambda = 0.05 sc_alpha= 0.7 sc_power= 1 couple-moltype = Protein couple-lambda0 = none couple-lambda1 = vdw-q grompp works fine, but mdrun (2 threads) gives me Making 1D domain decomposition 1 x 1 x 2 *** glibc detected *** mdrun: realloc(): invalid next size: 0x7f0f30305810 *** and breaks up. When running mdrun -nt 1 on only one thread, it works fine. Is this a known bug? Cheers Sabine -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] REMD equilibration
francesco oteri wrote: I understand, I am planning to run REMD between 300 and 600 K, so I think it is better equlibrating in NVT ensemble because at high temperature water evaporates, is it? Another very real concern is the stability of the simulations under NPT. At higher temperatures, the box itself may vary more widely and when the system is exchanged, the algorithms can fail. This phenomenon has been reported by a number of other users. With NVT, this does not happen. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] BUG: Free energy calculation
On 23/03/2012 9:17 PM, Sabine Reisser wrote: Dear gromacs users/developers, when trying to couple in a peptide into a membrane with: ; Define position restraints for peptide define = -DPOSRES ; couple in peptide free_energy = yes init_lambda = 0.05 sc_alpha= 0.7 sc_power= 1 couple-moltype = Protein couple-lambda0 = none couple-lambda1 = vdw-q grompp works fine, but mdrun (2 threads) gives me Making 1D domain decomposition 1 x 1 x 2 *** glibc detected *** mdrun: realloc(): invalid next size: 0x7f0f30305810 *** and breaks up. When running mdrun -nt 1 on only one thread, it works fine. Is this a known bug? First, is it likely not to be a problem with your setup... is your system stable in parallel without FE code? Without position restraints? What does your .log file say? What GROMACS version is it? 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Neigborsearching, Electrostatics and vdw options
Hi, *quote from a paper: A twin range cut-off for van der Waals (0.9/1.4 nm) and a smooth particle mesh Ewald algorithm for Coulomb interactions (switching distance of 0.9 nm) were used.* i.e.this means: ; NEIGHBORSEARCHING PARAMETERS . rlist = 0.9 ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype = PME rcoulomb = 0.9 vdw-type = Cut-off rvdw = 1.4 Am I wrong? A twin range cut-off for van der Waals (0.9/1.4 nm) means rlist/rvdw. isnt it?* * Thanks in advance* * 22 Mart 2012 01:32 tarihinde Oliver Stueker ostue...@gmail.com yazdı: Hi Ahmet, Let's imagine a sphere(two concentric spheres): radius of the inside small sphere=rvdw radius of the big sphere=rcoulomb distance between two of our nested spheres:rlist is this approach correct? No. I suggest you read section 4.6.3 (and probably also 4.6.2) in the Gromacs Manual. The Difference between rcoulomb (or rvdw) and rlist is a buffer-zone for the fact that the neighbor-lists are only updated every nstlist steps (often nstlist = 5). Oliver 2012/3/21 ahmet yıldırım ahmedo...@gmail.com: Dear users, Berk Hess says: [gmx-users] a) rlist vs rvdw/rcoulomb size confusion, and b) reduced units Mon Jul 16 14:17:12 CEST 2007 There are three options in Gromacs. The option you want is rcoulomb rlist and rvdw rlist. This works and gives the most accurate and also the most costly integration. A faster and very commonly used setting is: rlist=rcoulomb=rvdw. With PME the Coulomb interactions are very small at the cut-off, as are the LJ interactions. So with a small sacrifice in integration accuracy one can gain a lot of performance, also because analytical LJ is cheaper than tabulated. The last option is rcoulomb rlist and/or rvdw rlist. Then the energies and forces beyond rlist are only updated every nslist steps. This gives less integration accuracy but can give a lot of interaction accuracy at a small computational cost. Justin A. Lemkul says: [gmx-users] Twin-range cut-off Tue Sep 13 01:25:28 CEST 2011 A twin-range cutoff just means that your short-range cutoffs aren't all the same value, such that they form two interaction zones. Within the shortest, the neighbor list is updated every step. Between the shortest and longest cutoffs, the neighbor list is updated every nstlist steps. For instance: rlist = 0.9 rcoulomb = 0.9 rvdw = 1.4 are common settings for Gromos96 force fields (in conjunction with PME). Thus there are two interaction zones - the first is if two atoms (or charge groups, depending on the algorithm) are within 0.9 nm, and the second is if the two interacting species are beyond 0.9 nm but within 1.4 nm of each other. rcoulomb: distance for Coulomb cut-off (nm) rvdw:distance for LJ or Buckingham cut-off (nm) nstlist: neighbor list update frequency rlist: cut-off distance of the short-range neighbor Twin range cutoff consists of rcoulomb and rvdw, isnt it? Let's imagine a sphere(two concentric spheres): radius of the inside small sphere=rvdw radius of the big sphere=rcoulomb distance between two of our nested spheres:rlist is this approach correct? I could not understand the fourierspacing and rlist. Thanks in advance 21 Mart 2012 20:53 tarihinde ahmet yıldırım ahmedo...@gmail.com yazdı: Dear users, I have two configuration as the following related to Neigborsearching, Electrostatics and vdw options. I checked the literature: Generally the rlist, rcoulomb and rvdw have used as the following. rlist=1 rcoulomb=0.8 rvdw=1.4 Is there much difference between the following two options in the calculation/the results? Is there one significant difference between the two options. If yes, then what is it? What is relationship between rlist, nstlist and rvdw/rcoulomb? Furthermore, fourierspacing = 0.16 or fourierspacing = 0.12 difference between these two options? 1.choice . ; NEIGHBORSEARCHING PARAMETERS nstlist = 5 ns-type = Grid pbc= xyz rlist= 1.0 ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype = PME pme_order= 4 fourierspacing = 0.16 rcoulomb = 1.0 vdw-type = Cut-off rvdw = 1.0 ... 2.choice .. ; NEIGHBORSEARCHING PARAMETERS nstlist = 5 ns-type= Grid pbc = xyz rlist = 0.9 ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype = PME pme_order = 4 fourierspacing = 0.16 rcoulomb = 0.9 vdw-type = Cut-off rvdw = 1.4 ... Thanks in advance -- Ahmet Yıldırım --
Re: [gmx-users] BUG: Free energy calculation
Hi Mark, with FE, without PR : same error without FE, with PR: stable without FE, without PR: stable I've never had this error before. Logfile says: [...] Initializing Domain Decomposition on 2 nodes Dynamic load balancing: no Will sort the charge groups at every domain (re)decomposition Initial maximum inter charge-group distances: two-body bonded interactions: 3.341 nm, LJC Pairs NB, atoms 22476 22761 multi-body bonded interactions: 0.649 nm, Angle, atoms 1668 1686 Minimum cell size due to bonded interactions: 3.675 nm Using 0 separate PME nodes Optimizing the DD grid for 2 cells with a minimum initial size of 3.675 nm The maximum allowed number of cells is: X 1 Y 1 Z 2 Domain decomposition grid 1 x 1 x 2, separate PME nodes 0 PME domain decomposition: 2 x 1 x 1 Domain decomposition nodeid 0, coordinates 0 0 0 [...] Linking all bonded interactions to atoms There are 55376 inter charge-group exclusions, will use an extra communication step for exclusion forces for PME The initial number of communication pulses is: Z 1 The initial domain decomposition cell size is: Z 5.09 nm The maximum allowed distance for charge groups involved in interactions is: non-bonded interactions 1.200 nm two-body bonded interactions (-rdd) 4.213 nm multi-body bonded interactions (-rdd) 4.213 nm There it stops. In the 1-thread case, the second part is replaced by Initiating Steepest Descents and then writing out the energies for every step. Gromacs version is 4.5.5. I also attached the whole logfile. Cheers Sabine On 03/23/2012 11:52 AM, Mark Abraham wrote: On 23/03/2012 9:17 PM, Sabine Reisser wrote: Dear gromacs users/developers, when trying to couple in a peptide into a membrane with: ; Define position restraints for peptide define = -DPOSRES ; couple in peptide free_energy = yes init_lambda = 0.05 sc_alpha= 0.7 sc_power= 1 couple-moltype = Protein couple-lambda0 = none couple-lambda1 = vdw-q grompp works fine, but mdrun (2 threads) gives me Making 1D domain decomposition 1 x 1 x 2 *** glibc detected *** mdrun: realloc(): invalid next size: 0x7f0f30305810 *** and breaks up. When running mdrun -nt 1 on only one thread, it works fine. Is this a known bug? First, is it likely not to be a problem with your setup... is your system stable in parallel without FE code? Without position restraints? What does your .log file say? What GROMACS version is it? Mark Log file opened on Fri Mar 23 12:07:20 2012 Host: tcbpc170 pid: 4388 nodeid: 0 nnodes: 1 The Gromacs distribution was built Fri Feb 24 15:27:34 CET 2012 by sabine@tcbpc170 (Linux 2.6.30.10-105.2.23.fc11.x86_64 x86_64) :-) G R O M A C S (-: Giving Russians Opium May Alter Current Situation :-) VERSION 4.5.5 (-: Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Berk Hess, David van der Spoel, and Erik Lindahl. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2010, The GROMACS development team at Uppsala University The Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) mdrun (-: PLEASE READ AND CITE THE FOLLOWING REFERENCE B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation J. Chem. Theory Comput. 4 (2008) pp. 435-447 --- Thank You --- PLEASE READ AND CITE THE FOLLOWING REFERENCE D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C. Berendsen GROMACS: Fast, Flexible and Free J. Comp. Chem. 26 (2005) pp. 1701-1719 --- Thank You --- PLEASE READ AND CITE THE FOLLOWING REFERENCE E. Lindahl and B. Hess and D. van der Spoel GROMACS 3.0: A package for molecular simulation and trajectory analysis J. Mol. Mod. 7 (2001) pp. 306-317 --- Thank You --- PLEASE READ AND CITE THE FOLLOWING REFERENCE H. J. C. Berendsen, D. van der Spoel and R. van Drunen GROMACS: A message-passing parallel molecular dynamics implementation Comp. Phys. Comm. 91
Re: [gmx-users] BUG: Free energy calculation
Hi, Sabine- If you can go to http://redmine.gromacs.org/projects/gromacs/issues and file a bug report (including attaching files), I can look at it. If that's ends up not working well, you can send me the files off of the list, but it's usually better to have things in the redmine system so problems are documented. I'm also working on the updates to free energy code in 4.6, so I want to make sure this will be solved there as well. Best, Michael On Fri, Mar 23, 2012 at 7:16 AM, Sabine Reisser sabine.reis...@kit.edu wrote: Hi Mark, with FE, without PR : same error without FE, with PR: stable without FE, without PR: stable I've never had this error before. Logfile says: [...] Initializing Domain Decomposition on 2 nodes Dynamic load balancing: no Will sort the charge groups at every domain (re)decomposition Initial maximum inter charge-group distances: two-body bonded interactions: 3.341 nm, LJC Pairs NB, atoms 22476 22761 multi-body bonded interactions: 0.649 nm, Angle, atoms 1668 1686 Minimum cell size due to bonded interactions: 3.675 nm Using 0 separate PME nodes Optimizing the DD grid for 2 cells with a minimum initial size of 3.675 nm The maximum allowed number of cells is: X 1 Y 1 Z 2 Domain decomposition grid 1 x 1 x 2, separate PME nodes 0 PME domain decomposition: 2 x 1 x 1 Domain decomposition nodeid 0, coordinates 0 0 0 [...] Linking all bonded interactions to atoms There are 55376 inter charge-group exclusions, will use an extra communication step for exclusion forces for PME The initial number of communication pulses is: Z 1 The initial domain decomposition cell size is: Z 5.09 nm The maximum allowed distance for charge groups involved in interactions is: non-bonded interactions 1.200 nm two-body bonded interactions (-rdd) 4.213 nm multi-body bonded interactions (-rdd) 4.213 nm There it stops. In the 1-thread case, the second part is replaced by Initiating Steepest Descents and then writing out the energies for every step. Gromacs version is 4.5.5. I also attached the whole logfile. Cheers Sabine On 03/23/2012 11:52 AM, Mark Abraham wrote: On 23/03/2012 9:17 PM, Sabine Reisser wrote: Dear gromacs users/developers, when trying to couple in a peptide into a membrane with: ; Define position restraints for peptide define = -DPOSRES ; couple in peptide free_energy = yes init_lambda = 0.05 sc_alpha = 0.7 sc_power = 1 couple-moltype = Protein couple-lambda0 = none couple-lambda1 = vdw-q grompp works fine, but mdrun (2 threads) gives me Making 1D domain decomposition 1 x 1 x 2 *** glibc detected *** mdrun: realloc(): invalid next size: 0x7f0f30305810 *** and breaks up. When running mdrun -nt 1 on only one thread, it works fine. Is this a known bug? First, is it likely not to be a problem with your setup... is your system stable in parallel without FE code? Without position restraints? What does your .log file say? What GROMACS version is it? Mark -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Neigborsearching, Electrostatics and vdw options
ahmet yıldırım wrote: Hi, /quote from a paper: A twin range cut-off for van der Waals (0.9/1.4 nm) and a smooth particle mesh Ewald algorithm for Coulomb interactions (switching distance of 0.9 nm) were used./ i.e.this means: ; NEIGHBORSEARCHING PARAMETERS . rlist = 0.9 ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype = PME rcoulomb = 0.9 vdw-type = Cut-off rvdw = 1.4 Am I wrong? You are correct. A twin range cut-off for van der Waals (0.9/1.4 nm) means rlist/rvdw. isnt it?/ Yes. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] genbox
Hi all I have a system of 40 solute molecules in a solvent of 480 crown ether molecules. I am not trying to insert 100 methane molecules into this relaxed and well equilibrated structure using genbox. There are clearly visible cavities in the fluid but genbox only alllows the insertion of 8 methane molecules. How can I circumvent this problem ? The command I use is genbox -cp test.gro -ci methane.gro -nmol 100 -try 5 -p combined.top where combined.top includes all three itp files, and test.gro is the initial solute and solvent configuration. Cheers Gavin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] REMD equilibration
23 mar 2012 kl. 11.37 skrev Justin A. Lemkul: francesco oteri wrote: I understand, I am planning to run REMD between 300 and 600 K, so I think it is better equlibrating in NVT ensemble because at high temperature water evaporates, is it? Another very real concern is the stability of the simulations under NPT. At higher temperatures, the box itself may vary more widely and when the system is exchanged, the algorithms can fail. This phenomenon has been reported by a number of other users. With NVT, this does not happen. -Justin Very true. The benefit from NPT is on the other hand that the replicas can be more distant in temperature space, so if it works then NPT is more efficient. Erik -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] genbox
Gavin Melaugh wrote: Hi all I have a system of 40 solute molecules in a solvent of 480 crown ether molecules. I am not trying to insert 100 methane molecules into this relaxed and well equilibrated structure using genbox. There are clearly visible cavities in the fluid but genbox only alllows the insertion of 8 methane molecules. How can I circumvent this problem ? The command I use is genbox -cp test.gro -ci methane.gro -nmol 100 -try 5 -p combined.top where combined.top includes all three itp files, and test.gro is the initial solute and solvent configuration. You might try reducing the value used for -vdwd in genbox, or otherwise shrinking the vdW radii in vdwradii.dat, but be warned that if you have to finesse the system too much, likely any resulting simulation will be extremely temperamental, if you can even get it to run. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] BUG: Free energy calculation
Sabine Reisser wrote: Hi Mark, with FE, without PR : same error without FE, with PR: stable without FE, without PR: stable I've never had this error before. Logfile says: [...] Initializing Domain Decomposition on 2 nodes Dynamic load balancing: no Will sort the charge groups at every domain (re)decomposition Initial maximum inter charge-group distances: two-body bonded interactions: 3.341 nm, LJC Pairs NB, atoms 22476 22761 multi-body bonded interactions: 0.649 nm, Angle, atoms 1668 1686 Minimum cell size due to bonded interactions: 3.675 nm Using 0 separate PME nodes Optimizing the DD grid for 2 cells with a minimum initial size of 3.675 nm The maximum allowed number of cells is: X 1 Y 1 Z 2 Domain decomposition grid 1 x 1 x 2, separate PME nodes 0 PME domain decomposition: 2 x 1 x 1 Domain decomposition nodeid 0, coordinates 0 0 0 [...] Linking all bonded interactions to atoms There are 55376 inter charge-group exclusions, will use an extra communication step for exclusion forces for PME The initial number of communication pulses is: Z 1 The initial domain decomposition cell size is: Z 5.09 nm The maximum allowed distance for charge groups involved in interactions is: non-bonded interactions 1.200 nm two-body bonded interactions (-rdd) 4.213 nm multi-body bonded interactions (-rdd) 4.213 nm These quantities look very weird to me. They indicate interactions that are very far apart are influencing one another. Can you provide a complete .mdp file? It seems like some aspect of the free energy settings (perhaps couple-intramol?) and DD aren't getting along. The other possibility is to try particle decomposition instead of DD (i.e. mdrun -pd). -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] refcoord_scaling
Dear All, For the npt.mdp downloaded from the Justin Lemkul tutorial, it seems we need to add a line of refcoord_scaling. If so, its value should be all or com? I am looking forward to getting a reply from you. Cheers, Acoot -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] refcoord_scaling
Acoot Brett wrote: Dear All, For the npt.mdp downloaded from the Justin Lemkul tutorial, it seems we need to add a line of refcoord_scaling*.* If so, its value should be all or com? I am looking forward to getting a reply from you. Either should work. I doubt that for this case there would be a significant difference between the two. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Charmm Cholesterol parameters - str to itp
Hi GMX-users, Klauda et al (J. Phys. Chem. B, 2012, 116 (1), pp 203–210) recently provided Cholesterol parameters for Charmm FF. Does anyone know/have a protocol or script to convert the .str file to a valid .itp file for Charmm within GROMACS? I understand that Dr. Spoel and colleagues (J. Am. Chem. Soc., 2012, DOI: 10.1021/ja211929h) are providing cholesterol .itp for OPLS-AA. Could that maybe be a different starting point? Thanks for eventual reply, Ricardo. --- Ricardo O. S. Soares , PhD Student. Group of Biological Physics - Department of Physics Chemistry Faculty of Pharmaceutical Sciences at Ribeirão Preto - University of São Paulo. Av.do Café, S/N - ZIP:14040-903 - Ribeirão Preto, São Paulo, Brazil. Phone: +55 16 36024840. . .-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] BUG: Free energy calculation
Sabine, thanks for filing it in redmine! Having a record helps a lot. Can you also attach all your input files to the redmine filing? It can only really be debugged if the input files you used are included. Best, Michael On Fri, Mar 23, 2012 at 9:11 AM, Justin A. Lemkul jalem...@vt.edu wrote: Sabine Reisser wrote: Hi Mark, with FE, without PR : same error without FE, with PR: stable without FE, without PR: stable I've never had this error before. Logfile says: [...] Initializing Domain Decomposition on 2 nodes Dynamic load balancing: no Will sort the charge groups at every domain (re)decomposition Initial maximum inter charge-group distances: two-body bonded interactions: 3.341 nm, LJC Pairs NB, atoms 22476 22761 multi-body bonded interactions: 0.649 nm, Angle, atoms 1668 1686 Minimum cell size due to bonded interactions: 3.675 nm Using 0 separate PME nodes Optimizing the DD grid for 2 cells with a minimum initial size of 3.675 nm The maximum allowed number of cells is: X 1 Y 1 Z 2 Domain decomposition grid 1 x 1 x 2, separate PME nodes 0 PME domain decomposition: 2 x 1 x 1 Domain decomposition nodeid 0, coordinates 0 0 0 [...] Linking all bonded interactions to atoms There are 55376 inter charge-group exclusions, will use an extra communication step for exclusion forces for PME The initial number of communication pulses is: Z 1 The initial domain decomposition cell size is: Z 5.09 nm The maximum allowed distance for charge groups involved in interactions is: non-bonded interactions 1.200 nm two-body bonded interactions (-rdd) 4.213 nm multi-body bonded interactions (-rdd) 4.213 nm These quantities look very weird to me. They indicate interactions that are very far apart are influencing one another. Can you provide a complete .mdp file? It seems like some aspect of the free energy settings (perhaps couple-intramol?) and DD aren't getting along. The other possibility is to try particle decomposition instead of DD (i.e. mdrun -pd). -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] parameters of em.mdp
Dear users, I am using the Reaction-Field method for electrostatics interactions. I used the following parameters for all input files (em.mdp, pr.mdp, nvt.mdp, npt.mdp, md.mdp). I just changed as an epsilon_rf=78 in md.mdp. If I set nstlist=rlist=rcoulomb=rvdw=1.0 for energy minimization, would not it be better? What is your suggestions? ; Neighbor Searching Parameters nstlist = 5 ns-type = Grid pbc= xyz rlist = 0.9 ; Electrostatics coulombtype = Reaction-Field rcoulomb= 1.4 epsilon_rf = 54 ; VdW vdw-type= Cut-off rvdw= 1.4 * Another question:* I used 200 K (in pr.mdp) and 300 K (in nvt.mdp, npt.mdp and md.mdp) the reference temperature for coupling. I analysed the temperature after production run. I get Temperature=312.646 (g_energy -f md.edr -o temperature.xvg). that is, The temperature has increased (approximately 12 K) during the simulation. What could be the reason for the increase in temperature? I had setted to 200 K the reference temperature for coupling in pr.mdp. it can cause? My em.mdp file is as the following: *em.mdp:* title= Energy Minimization ; Title of run cpp= /lib/cpp ; Preprocessor: Line tell the program the standard locations where to find certain files define = -DFLEXIBLE ; defines to pass to the preprocessor ; Run Control integrator= steep; steep integrator (steep = steepest descent minimization) nsteps= 2500; maximum number of steps to integrate ; Energy Minimization emtol= 1000.0 ; [kJ/mol/nm] minimization is converged when max force is emtol emstep = 0.01 ; [nm] initial step-size ; Output Control nstxout = 0 ; [steps] freq to write coordinates to trajectory nstvout = 0 ; [steps] freq to write velocities to trajectory nstfout = 0 ; [steps] freq to write forces to trajectory nstlog = 1 ; [steps] freq to write energies to log file nstenergy= 1; [steps] freq to write energies to energy file energygrps= System; group(s) to write to energy file ; Neighbor Searching Parameters nstlist = 5 ; [steps] freq to update neighbor list ns-type = Grid ; method of updating neighbor list pbc= xyz; periodic boundary conditions (yes/no)in all directions rlist = 0.9 ; [nm] cut-off distance for the short-range neighbor list ; Electrostatics coulombtype = Reaction-Field ; Reaction-Field electrostatics rcoulomb= 1.4 ; [nm] distance for Coulomb cut-off epsilon_rf = 54 ; The relative dielectric constant of the reaction field ; VdW vdw-type= Cut-off ; twin-range cut-off with rlist where rvdw = rlist rvdw= 1.4 ; [nm] distance for LJ cut-off ; Bonds constraints = none ; convert all bonds to constraints -- Ahmet Yıldırım -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Charmm Cholesterol parameters - str to itp
On 2012-03-23 15:31, Ricardo O. S. Soares wrote:
Hi GMX-users,
Klauda et al (J. Phys. Chem. B, 2012, 116(1), pp 203–210) recently
provided Cholesterol parameters for Charmm FF.
Does anyone know/have a protocol or script to convert the .str file to a
valid .itp file for Charmm within GROMACS?
I understand that Dr. Spoel and colleagues (*J. Am. Chem. Soc.*, 2012,
DOI: 10.1021/ja211929h) are providing cholesterol .itp for OPLS-AA.
Could that maybe be a different starting point?
Thanks for eventual reply,
Here's a script that has been used for this purpose. Please use with
care and *check your output*.
Ricardo.
---
Ricardo O. S. Soares , PhD Student.
Group of Biological Physics - Department of Physics Chemistry
Faculty of Pharmaceutical Sciences at Ribeirão Preto - University of São
Paulo.
Av.do Café, S/N - ZIP:14040-903 - Ribeirão Preto, São Paulo, Brazil.
Phone: +55 16 36024840.
.
.
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
#!/usr/bin/python
Script for parsing charmm force field to gromacs format
inparameters:
command line parameters:
1 charmm topology file
2 corresponding charmm parameter file
3 opt foldername, default cgenff.ff
outfiles:
1 foldername/atomtypes.atp
2 foldername/forcefield.itp
3 foldername/forcefield.doc
4 foldername/aminoacids.rtp
5 foldername/ffbonded.itp
6 foldername/ffnonbonded.itp
7 foldername/forcefield.r2b
8 opt foldername/lipids.rtp (if '!lipid section' statement in CHARMM top file)
9 opt foldername/cmap.itp (if genCMAP = True)
import sys
import math
import re
import os
#--
# System parameters
#--
# infiles
parFile = open(sys.argv[2], 'r')
topFile = open(sys.argv[1], 'r')
# test to see if there's a name specified
if len(sys.argv)3:
ffName = sys.argv[3]
print('Creating '+ffName+' files...')
# if not, use cgenff
else:
ffName = 'cgenff-2b7.ff'
print('Creating '+ffName+' files...')
# conversion constant between kcal and kJ
kcal2kJ = 4.184
#-
# User specific parameters
#-
# specification of character used for comments in charmm ff file
comment = '!'
# create folder for output files
os.mkdir(ffName)
os.chdir(ffName)
# outfiles
nbFile = open('ffnonbonded.itp', 'w') # nonbonded file
bonFile = open('ffbonded.itp', 'w') # bonded file
atpFile = open('atomtypes.atp', 'w') # atom type file
itpFile = open('forcefield.itp', 'w') # ffcharmm**.itp file
docFile = open('forcefield.doc', 'w') # ffcharmm**.itp file
aartpFile = open('aminoacids.rtp', 'w') # aminoacids rtp file
for line in topFile:
if line.startswith('CMAP'):
print \n NOTE: This force field seems to support CMAP so trying to port it!\n
genCMAP = True
cmapFile = open('cmap.itp', 'w') # cmap itp file
break
else:
genCMAP = False
topFile.close()
topFile = open('../'+sys.argv[1], 'r')
# set the func parameter for bonds, angles and proper/improper dihedrals
# for further information see section 5.3.2 in gromacs documentation:
# ftp://ftp.gromacs.org/pub/manual/manual-3.3.pdf
funcForBonds = '1'
funcForAngles = '5' # Urey-Bradley angle type
funcForDihedrals = '9' # special type for treating multiple entries (modification in source code)
funcForImpropers = '2'
funcFor14 = '1' # function
# particle type
ptype = 'A'
# dictionary for atom numbers, used for the nb file
element2atomNumber= {}
element2atomNumber['H']='1'
element2atomNumber['HE']='2'
element2atomNumber['C']='6'
element2atomNumber['N']='7'
element2atomNumber['O']='8'
element2atomNumber['F']='9'
element2atomNumber['NE']='10'
element2atomNumber['NA']='11'
element2atomNumber['MG']='12'
element2atomNumber['AL']='13'
element2atomNumber['P']='15'
element2atomNumber['S']='16'
element2atomNumber['CL']='17'
element2atomNumber['K']='19'
element2atomNumber['CA']='20'
element2atomNumber['Fe']='26'
element2atomNumber['ZN']='30'
element2atomNumber['BR']='35'
element2atomNumber['I']='53'
element2atomNumber['CS']='55'
#---
# parsing the charmm top file and writing to gromacs .atp and .rtp files
#---
# position flags
mass = False
postMass = False
type2element = {}
element2mass = {}
type2charge = {}
firstBond = True
firstImpr = True
presFlag = False
lipidFlag = False
lipidFlagCounter = 0
# group counter
groupCounter = 0
# initiation of rtp file, defaults etc
aartpFile.write('[ bondedtypes ] \n')
aartpFile.write('; Col 1: Type of bond \n')
aartpFile.write('; Col 2: Type of angles \n')
aartpFile.write('; Col 3: Type of proper dihedrals \n')
aartpFile.write('; Col 4: Type of improper dihedrals \n')
aartpFile.write('; Col 5: Generate all dihedrals if 1, only heavy atoms of 0. \n')
aartpFile.write('; Col 6: Number
Re: [gmx-users] parameters of em.mdp
ahmet yıldırım wrote: Dear users, I am using the Reaction-Field method for electrostatics interactions. I used the following parameters for all input files (em.mdp, pr.mdp, nvt.mdp, npt.mdp, md.mdp). I just changed as an epsilon_rf=78 in md.mdp. If I set nstlist=rlist=rcoulomb=rvdw=1.0 for energy minimization, would not it be better? What is your suggestions? Why do you think making such changes to the cutoffs would be better? These settings, for the most part, are a fixed part of the force field you're using. Unless you have proof (either by your own demonstration or one that is published) that making such changes result in better results, you should avoid ad hoc changes. ; Neighbor Searching Parameters nstlist = 5 ns-type = Grid pbc= xyz rlist = 0.9 ; Electrostatics coulombtype = Reaction-Field rcoulomb= 1.4 epsilon_rf = 54 ; VdW vdw-type= Cut-off rvdw= 1.4 * Another question:* I used 200 K (in pr.mdp) and 300 K (in nvt.mdp, npt.mdp and md.mdp) the reference temperature for coupling. I analysed the temperature after production run. I get Temperature=312.646 (g_energy -f md.edr -o temperature.xvg). that is, The temperature has increased (approximately 12 K) during the simulation. What could be the reason for the increase in temperature? I had setted to 200 K the reference temperature for coupling in pr.mdp. it can cause? This outcome is precisely what you would expect, simply because you're using the reaction field method and it introduces cutoff artifacts. Interestingly, this same outcome (an increase of exactly 12K) has been reported before: http://lists.gromacs.org/pipermail/gmx-users/2009-January/039113.html -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Charmm Cholesterol parameters - str to itp
De: David van der Spoel sp...@xray.bmc.uu.se Para: Discussion list for GROMACS users gmx-users@gromacs.org Enviadas: Sexta-feira, 23 de Março de 2012 14:31 Assunto: Re: [gmx-users] Charmm Cholesterol parameters - str to itp On 2012-03-23 15:31, Ricardo O. S. Soares wrote: Hi GMX-users, Klauda et al (J. Phys. Chem. B, 2012, 116(1), pp 203–210) recently provided Cholesterol parameters for Charmm FF. Does anyone know/have a protocol or script to convert the .str file to a valid .itp file for Charmm within GROMACS? I understand that Dr. Spoel and colleagues (*J. Am. Chem. Soc.*, 2012, DOI: 10.1021/ja211929h) are providing cholesterol .itp for OPLS-AA. Could that maybe be a different starting point? Thanks for eventual reply, Here's a script that has been used for this purpose. Please use with care and *check your output*. Thank you David, that is really helpful! I'll give it a try! Cheers Ricardo. --- Ricardo O. S. Soares , PhD Student. Group of Biological Physics - Department of Physics Chemistry Faculty of Pharmaceutical Sciences at Ribeirão Preto - University of São Paulo. Av.do Café, S/N - ZIP:14040-903 - Ribeirão Preto, São Paulo, Brazil. Phone: +55 16 36024840. . . -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.se http://folding.bmc.uu.se -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Equilibrate the water around my molecule
Hello I want to equilibrate the water around my (small) molecule. In the tutorials I found and in the manual is not enough information how to do that if you have an own parametrization of a molecule. Here is my situation: I have a pdb file and I have a parametrization for this molecule out of a supporting information from a paper. I create a .rtp and .hdb file, changed atomtypes.atp, ffnonbonded.itp and residuetypes.dat. In the .rtp file I called my molecule [ ISO ] before the [ atoms ] section starts. In the residuetypes.dat file I write ISO Isoalloxazin After that I did the calculation described in the tutorial of Erik Lindahl and I got no errors up to equilibrating the water around my molecule. In my pr.mdp file is the entry tc-grps = protein non-protein I guess this is a problem because I got an error and with best thanks I got this solution from Mark Abraham: http://lists.gromacs.org/pipermail/gmx-users/2012-March/069096.html I read something about make_ndx and about Thermostats but I still have no idea how to go forward with this problem :-( Please help Thanks and greetings Lara -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] parameters of em.mdp
Dear Justin, Thanks for your reply. You said You should avoid ad hoc changes. You used different parameters for energy minimization at tutorial called Tutorial 5: Protein-Ligand Complex. *a part of your em.mdp* nstlist = 1 rlist = 1.0 rcoulomb = 1.0 rvdw = 1.0 *a part of your md.mdp* nstlist = 5 rlist = 0.9 rcoulomb = 0.9 rvdw = 1.4 Then, Why did you change some parameters (nstlist,rlist,rcoulomb,rvdw) for energy minimization? Thanks in advance 23 Mart 2012 19:31 tarihinde Justin A. Lemkul jalem...@vt.edu yazdı: ahmet yıldırım wrote: Dear users, I am using the Reaction-Field method for electrostatics interactions. I used the following parameters for all input files (em.mdp, pr.mdp, nvt.mdp, npt.mdp, md.mdp). I just changed as an epsilon_rf=78 in md.mdp. If I set nstlist=rlist=rcoulomb=rvdw=1.**0 for energy minimization, would not it be better? What is your suggestions? Why do you think making such changes to the cutoffs would be better? These settings, for the most part, are a fixed part of the force field you're using. Unless you have proof (either by your own demonstration or one that is published) that making such changes result in better results, you should avoid ad hoc changes. ; Neighbor Searching Parameters nstlist = 5 ns-type = Grid pbc = xyz rlist = 0.9 ; Electrostatics coulombtype = Reaction-Field rcoulomb= 1.4 epsilon_rf = 54 ; VdW vdw-type= Cut-off rvdw= 1.4 * Another question:* I used 200 K (in pr.mdp) and 300 K (in nvt.mdp, npt.mdp and md.mdp) the reference temperature for coupling. I analysed the temperature after production run. I get Temperature=312.646 (g_energy -f md.edr -o temperature.xvg). that is, The temperature has increased (approximately 12 K) during the simulation. What could be the reason for the increase in temperature? I had setted to 200 K the reference temperature for coupling in pr.mdp. it can cause? This outcome is precisely what you would expect, simply because you're using the reaction field method and it introduces cutoff artifacts. Interestingly, this same outcome (an increase of exactly 12K) has been reported before: http://lists.gromacs.org/**pipermail/gmx-users/2009-**January/039113.htmlhttp://lists.gromacs.org/pipermail/gmx-users/2009-January/039113.html -Justin -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Ahmet Yıldırım -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Equilibrate the water around my molecule
On 24/03/2012 5:38 AM, Lara Bunte wrote: Hello I want to equilibrate the water around my (small) molecule. In the tutorials I found and in the manual is not enough information how to do that if you have an own parametrization of a molecule. Here is my situation: I have a pdb file and I have a parametrization for this molecule out of a supporting information from a paper. I create a .rtp and .hdb file, changed atomtypes.atp, ffnonbonded.itp and residuetypes.dat. In the .rtp file I called my molecule [ ISO ] before the [ atoms ] section starts. In the residuetypes.dat file I write ISO Isoalloxazin The above entry in residuetypes.dat makes it impossible for GROMACS to recognise your ISO as protein. See manual 8.1.1. This file identifies the *type* of the *residue* to permit GROMACS and you to agree on broad categorizations of residues. Telling GROMACS the full name of the molecule is not helpful here. After that I did the calculation described in the tutorial of Erik Lindahl and I got no errors up to equilibrating the water around my molecule. In my pr.mdp file is the entry tc-grps = protein non-protein Here you require a protein group to exist. Apparently you have no part of your system that is protein according to residuetypes.dat, and so there is no such group. If you'd had another protein element to your system, then grompp would have regarded ISO as non-protein, and you might have been left with a hard-to-notice problem. I guess this is a problem because I got an error and with best thanks I got this solution from Mark Abraham: http://lists.gromacs.org/pipermail/gmx-users/2012-March/069096.html I read something about make_ndx and about Thermostats but I still have no idea how to go forward with this problem :-( All three forms of solution I proposed there are still possible. The second is the easiest: use ISO Protein in your residuetypes.dat. 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] parameters of em.mdp
ahmet yıldırım wrote: Dear Justin, Thanks for your reply. You said You should avoid ad hoc changes. You used different parameters for energy minimization at tutorial called Tutorial 5: Protein-Ligand Complex. _*a part of your em.mdp*_ nstlist = 1 rlist = 1.0 rcoulomb = 1.0 rvdw = 1.0 _*a part of your md.mdp*_ nstlist = 5 rlist = 0.9 rcoulomb = 0.9 rvdw = 1.4 Then, Why did you change some parameters (nstlist,rlist,rcoulomb,rvdw) for energy minimization? In my experience, the outcome of EM is not particularly sensitive to those types of changes for very robust systems, especially in single precision. The energy values and maximum forces achieved don't change appreciably in most cases. Regarding nstlist, for EM it should be set to 1. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] CHARMM27 topology for DOPC
Hi GMX Users, I have generated a topology entry for the DOPC lipid for charmm27.ff/lipids.rtp by copying and editing the entry of POPC. My DOPC has passed two simple tests with gromacs-4.5.3 on a test structure of an isolated model molecule (generated with CHARMM) 1) energy minimization produced a reasonable structure close to starting coordinates 2) all energy components agreed with CHARMM v. 27 results to at least 4 digits. I enclose my topology file; I would welcome - information about other DOPC topologies in GMX - critical comments - suggestions for more simple tests ( the 100 ns solvated bilayer simulation is already on my list) Greetings Krzysztof Kuczera -- Krzysztof Kuczera Departments of Chemistry and Molecular Biosciences The University of Kansas 2010 Malott Hall Lawrence, KS 66045 Tel: 785-864-5060 Fax: 785-864-5396 email: kkucz...@ku.edu http://oolung.chem.ku.edu/~kuczera/home.html [ DOPC ] [ atoms ] N NTL -0.60 0 C11 CTL2-0.10 1 C12 CTL5-0.35 2 C13 CTL5-0.35 3 C14 CTL5-0.35 4 H11 HL 0.255 H12 HL 0.256 H21 HL 0.257 H22 HL 0.258 H23 HL 0.259 H31 HL 0.2510 H32 HL 0.2511 H33 HL 0.2512 H41 HL 0.2513 H42 HL 0.2514 H43 HL 0.2515 C15 CTL2-0.08 16 H51 HAL20.0917 H52 HAL20.0918 P1 PL 1.5019 O3 O2L -0.78 20 O4 O2L -0.78 21 O1 OSL -0.57 22 O2 OSL -0.57 23 C1 CTL2-0.08 24 HA HAL20.0925 HB HAL20.0926 C2 CTL10.0427 HS HAL10.0928 O21 OSL -0.34 29 C21 CL 0.6330 O22 OBL -0.52 31 C22 CTL2-0.08 32 H2R HAL20.0933 H2S HAL20.0934 C3 CTL2-0.05 35 HX HAL20.0936 HY HAL20.0937 O31 OSL -0.34 38 C31 CL 0.6339 O32 OBL -0.52 40 C32 CTL2-0.08 41 H2X HAL20.0942 H2Y HAL20.0943 C23 CTL2-0.18 44 H3R HAL20.0945 H3S HAL20.0946 C24 CTL2-0.18 47 H4R HAL20.0948 H4S HAL20.0949 C25 CTL2-0.18 50 H5R HAL20.0951 H5S HAL20.0952 C26 CTL2-0.18 53 H6R HAL20.0954 H6S HAL20.0955 C27 CTL2-0.18 56 H7R HAL20.0957 H7S HAL20.0958 C28 CTL2-0.18 59 H8R HAL20.0960 H8S HAL20.0961 C29 CEL1-0.15 62 H91 HEL10.1563 C210CEL1-0.15 64 H101HEL10.1565 C211CTL2-0.18 66 H11RHAL20.0967 H11SHAL20.0968 C212CTL2-0.18 69 H12RHAL20.0970 H12SHAL20.0971 C213CTL2-0.18 72 H13RHAL20.0973 H13SHAL20.0974 C214CTL2-0.18 75 H14RHAL20.0976 H14SHAL20.0977 C215CTL2-0.18 78 H15RHAL20.0979 H15SHAL20.0980 C216CTL2-0.18 81 H16RHAL20.0982 H16SHAL20.0983 C217CTL2-0.18 84 H17RHAL20.0985 H17SHAL20.0986 C218CTL3-0.27 87 H18RHAL30.0988 H18SHAL30.0989 H18THAL30.0990 C33 CTL2-0.18 91 H3X HAL20.0992 H3Y HAL20.0993 C34 CTL2-0.18 94 H4X HAL20.0995 H4Y HAL20.0996 C35 CTL2-0.18 97 H5X HAL20.0998 H5Y HAL20.0999 C36 CTL2-0.18 100 H6X HAL20.09101 H6Y HAL20.09102 C37 CTL2-0.18 103 H7X HAL20.09104 H7Y HAL20.09105 C38 CTL2-0.18 106 H8X HAL20.09107 H8Y HAL20.09108 C39 CEL1-0.15 109 H92 HEL10.15110 C310CEL1-0.15 111 H102HEL10.15112 C311CTL2-0.18 113 H11XHAL20.09114 H11Y
[gmx-users] Do checkpoint files contain energies?
Hi, If you have time, can you please tell me if checkpoint (.cpt) files contain data on energies? Suppose I have a checkpoint file check.cpt, which I obtained by using the -cpo flag of mdrun. Now suppose I want to continue the run using a new .mdp file (not just extend it, http://www.gromacs.org/Documentation/How-tos/Extending_Simulations), but using the same ensemble (NVT) and reference temperature. If I now use the commands: --- grompp -f newgrompp.mdp -c conf.gro -p topol.top -o newrun.tpr -t check.cpt mdrun -deffnm newrun --- where newgrompp.mdp contains continuation = yes and gen_vel = no, will the energies be continuous across the runs? Or should I also include the -e flag in my new call to grompp, in addition to the -t flag? --- grompp -f newgrompp.mdp -c conf.gro -p topol.top -o newrun.tpr -t check.cpt -e ener.edr mdrun -deffnm newrun --- assuming that ener.edr was the energy output from the first mdrun (the commands for which I am not showing). When I use gmxcheck -f check.cpt, I get this output: --- # Atoms 6144 Last frame -1 time 600.000 Item#frames Timestep (ps) Step 1 Time 1 Lambda 1 Coords 1 Velocities 1 Forces 0 Box 1 --- so it is not clear to me whether the .cpt file contains information about the energy. gmxdump will not read checkpoint files (it says File check.cpt is of an unsupported type. Try using the command 'less check.cpt' if I use gmxdump -f check.cpt; when I use less check.cpt, I just get nonsense characters as less attempts to read binary). Thank you very much for your time! Andrew DeYoung Carnegie Mellon 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] CHARMM27 topology for DOPC
Compare and contrast with Klauda et al. Phys Chem. B, 2010, 114, 7830 ? On 2012-03-23 02:28:45PM -0500, Krzysztof Kuczera wrote: Hi GMX Users, I have generated a topology entry for the DOPC lipid for charmm27.ff/lipids.rtp by copying and editing the entry of POPC. My DOPC has passed two simple tests with gromacs-4.5.3 on a test structure of an isolated model molecule (generated with CHARMM) 1) energy minimization produced a reasonable structure close to starting coordinates 2) all energy components agreed with CHARMM v. 27 results to at least 4 digits. I enclose my topology file; I would welcome - information about other DOPC topologies in GMX - critical comments - suggestions for more simple tests ( the 100 ns solvated bilayer simulation is already on my list) Greetings Krzysztof Kuczera -- Krzysztof Kuczera Departments of Chemistry and Molecular Biosciences The University of Kansas 2010 Malott Hall Lawrence, KS 66045 Tel: 785-864-5060 Fax: 785-864-5396 email: kkucz...@ku.edu http://oolung.chem.ku.edu/~kuczera/home.html [ DOPC ] [ atoms ] N NTL -0.60 0 C11 CTL2-0.10 1 C12 CTL5-0.35 2 C13 CTL5-0.35 3 C14 CTL5-0.35 4 H11 HL 0.255 H12 HL 0.256 H21 HL 0.257 H22 HL 0.258 H23 HL 0.259 H31 HL 0.2510 H32 HL 0.2511 H33 HL 0.2512 H41 HL 0.2513 H42 HL 0.2514 H43 HL 0.2515 C15 CTL2-0.08 16 H51 HAL20.0917 H52 HAL20.0918 P1 PL 1.5019 O3 O2L -0.78 20 O4 O2L -0.78 21 O1 OSL -0.57 22 O2 OSL -0.57 23 C1 CTL2-0.08 24 HA HAL20.0925 HB HAL20.0926 C2 CTL10.0427 HS HAL10.0928 O21 OSL -0.34 29 C21 CL 0.6330 O22 OBL -0.52 31 C22 CTL2-0.08 32 H2R HAL20.0933 H2S HAL20.0934 C3 CTL2-0.05 35 HX HAL20.0936 HY HAL20.0937 O31 OSL -0.34 38 C31 CL 0.6339 O32 OBL -0.52 40 C32 CTL2-0.08 41 H2X HAL20.0942 H2Y HAL20.0943 C23 CTL2-0.18 44 H3R HAL20.0945 H3S HAL20.0946 C24 CTL2-0.18 47 H4R HAL20.0948 H4S HAL20.0949 C25 CTL2-0.18 50 H5R HAL20.0951 H5S HAL20.0952 C26 CTL2-0.18 53 H6R HAL20.0954 H6S HAL20.0955 C27 CTL2-0.18 56 H7R HAL20.0957 H7S HAL20.0958 C28 CTL2-0.18 59 H8R HAL20.0960 H8S HAL20.0961 C29 CEL1-0.15 62 H91 HEL10.1563 C210CEL1-0.15 64 H101HEL10.1565 C211CTL2-0.18 66 H11RHAL20.0967 H11SHAL20.0968 C212CTL2-0.18 69 H12RHAL20.0970 H12SHAL20.0971 C213CTL2-0.18 72 H13RHAL20.0973 H13SHAL20.0974 C214CTL2-0.18 75 H14RHAL20.0976 H14SHAL20.0977 C215CTL2-0.18 78 H15RHAL20.0979 H15SHAL20.0980 C216CTL2-0.18 81 H16RHAL20.0982 H16SHAL20.0983 C217CTL2-0.18 84 H17RHAL20.0985 H17SHAL20.0986 C218CTL3-0.27 87 H18RHAL30.0988 H18SHAL30.0989 H18THAL30.0990 C33 CTL2-0.18 91 H3X HAL20.0992 H3Y HAL20.0993 C34 CTL2-0.18 94 H4X HAL20.0995 H4Y HAL20.0996 C35 CTL2-0.18 97 H5X HAL20.0998 H5Y HAL20.0999 C36 CTL2-0.18 100 H6X HAL20.09101 H6Y HAL20.09102 C37 CTL2-0.18 103 H7X HAL20.09104 H7Y HAL20.09105 C38 CTL2-0.18 106 H8X HAL20.09107 H8Y HAL20.09108 C39 CEL1-0.15 109 H92 HEL10.15110 C310CEL1-0.15 111 H102HEL10.15112 C311CTL2-0.18 113
[gmx-users] Fatal error: Atom CG is used in the topology database...
Hi All, I'm trying to generate topology for a PDB from viperdb, PDB ID 1DZL, http://viperdb.scripps.edu/info_page.php?VDB=1dzl using pdb2gmx -f 1dzl_full.pdb -o test.pdb -p test.top I've tried CHARMM27 and AMBER03 FFs, water none and I get the result: Fatal error: Atom CG is used in the topology database, but an atom of that name was not found in residue number 1. I have not have much luck finding this error in any mailing list. If the PDB does have missing atoms, can pdb2gmx guess missing atoms like VMD's psf gen? Any ideas? 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Do checkpoint files contain energies?
Andrew DeYoung wrote: Hi, If you have time, can you please tell me if checkpoint (.cpt) files contain data on energies? Yes, it does. Suppose I have a checkpoint file check.cpt, which I obtained by using the -cpo flag of mdrun. Now suppose I want to continue the run using a new .mdp file (not just extend it, http://www.gromacs.org/Documentation/How-tos/Extending_Simulations), but using the same ensemble (NVT) and reference temperature. If I now use the commands: --- grompp -f newgrompp.mdp -c conf.gro -p topol.top -o newrun.tpr -t check.cpt mdrun -deffnm newrun --- where newgrompp.mdp contains continuation = yes and gen_vel = no, will the energies be continuous across the runs? Or should I also include the -e flag in my new call to grompp, in addition to the -t flag? The checkpoint should be all that is necessary. --- grompp -f newgrompp.mdp -c conf.gro -p topol.top -o newrun.tpr -t check.cpt -e ener.edr mdrun -deffnm newrun --- assuming that ener.edr was the energy output from the first mdrun (the commands for which I am not showing). When I use gmxcheck -f check.cpt, I get this output: --- # Atoms 6144 Last frame -1 time 600.000 Item#frames Timestep (ps) Step 1 Time 1 Lambda 1 Coords 1 Velocities 1 Forces 0 Box 1 --- so it is not clear to me whether the .cpt file contains information about the energy. gmxdump will not read checkpoint files (it says File check.cpt is of an unsupported type. Try using the command 'less check.cpt' if I use gmxdump -f check.cpt; when I use less check.cpt, I just get nonsense characters as less attempts to read binary). What you want is gmxdump -cp check.cpt - the very end of the file has all the energies, written in a manner similar to how they are present in an .edr file. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Fatal error: Atom CG is used in the topology database...
Andy Somogyi wrote: Hi All, I'm trying to generate topology for a PDB from viperdb, PDB ID 1DZL, http://viperdb.scripps.edu/info_page.php?VDB=1dzl using pdb2gmx -f 1dzl_full.pdb -o test.pdb -p test.top I've tried CHARMM27 and AMBER03 FFs, water none and I get the result: Fatal error: Atom CG is used in the topology database, but an atom of that name was not found in residue number 1. I have not have much luck finding this error in any mailing list. I've never seen that error before, but it sounds like there is an atom named 'CG' in the .rtp entry but not in the coordinate file. Either the atom is named differently or it is missing. If the PDB does have missing atoms, can pdb2gmx guess missing atoms like VMD's psf gen? No. The contents of the input coordinate file must match what is expected by the .rtp file. If you have missing atoms, they must be modeled in using external software. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Fatal error: Atom CG is used in the topology database...
On 2012-03-23 05:39:38PM -0400, Justin A. Lemkul wrote: Andy Somogyi wrote: Hi All, I'm trying to generate topology for a PDB from viperdb, PDB ID 1DZL, http://viperdb.scripps.edu/info_page.php?VDB=1dzl using pdb2gmx -f 1dzl_full.pdb -o test.pdb -p test.top I've tried CHARMM27 and AMBER03 FFs, water none and I get the result: Fatal error: Atom CG is used in the topology database, but an atom of that name was not found in residue number 1. I have not have much luck finding this error in any mailing list. I've never seen that error before, but it sounds like there is an atom named 'CG' in the .rtp entry but not in the coordinate file. Either the atom is named differently or it is missing. If the PDB does have missing atoms, can pdb2gmx guess missing atoms like VMD's psf gen? No. The contents of the input coordinate file must match what is expected by the .rtp file. If you have missing atoms, they must be modeled in using external software. I wonder if there is a way to overload the hydrogen-adding mechanism to add heavy atoms too. -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] renumber charge group
Dear user, Please see attached file. I renumbered the cgnr of a ligand. Is there any mistake related to renumbered of cgnr? I get the following error when I run position restrain (pr.mdp) mdrun -deffnm pr Fatal error: A charge group moved too far between two domain decomposition steps This usually means that your system is not well equilibrated [ moleculetype ] ; Name nrexcl TRIS 3 [ atoms ] ; nr type resnr resid atom cgnr chargemasstotal_charge 1 CH01TRIS C10.143 12.0110 2NL1TRIS N1 -0.590 14.0067 3 H1TRIS H10.399 1.0080 4 H1TRIS H10.399 1.0080 5 H1TRIS H10.399 1.0080 6 CH21TRIS C20.257 14.0270 7OA1TRIS O2 -0.637 15.9994 8 H1TRIS H20.463 1.0080 9 CH21TRIS C30.257 14.0270 10OA1TRIS O3 -0.637 15.9994 11 H1TRIS H30.463 1.0080 12 CH21TRIS C40.257 14.0270 13OA1TRIS O4 -0.636 15.9994 14 H1TRIS H40.463 1.0080 ; 1.000 ; total charge of the molecule: 1.000 -- Ahmet Yıldırım attachment: TRIS.png-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] renumber charge group
ahmet yıldırım wrote: Dear user, Please see attached file. I renumbered the cgnr of a ligand. Is there any mistake related to renumbered of cgnr? I see nothing unreasonable. I get the following error when I run position restrain (pr.mdp) mdrun -deffnm pr Fatal error: A charge group moved too far between two domain decomposition steps This usually means that your system is not well equilibrated The error simply means you have atoms flying across your unit cell, thus it is blowing up. http://www.gromacs.org/Documentation/Terminology/Blowing_Up -Justin [ moleculetype ] ; Name nrexcl TRIS 3 [ atoms ] ; nr type resnr resid atom cgnr chargemasstotal_charge 1 CH01TRIS C10.143 12.0110 2NL1TRIS N1 -0.590 14.0067 3 H1TRIS H10.399 1.0080 4 H1TRIS H10.399 1.0080 5 H1TRIS H10.399 1.0080 6 CH21TRIS C20.257 14.0270 7OA1TRIS O2 -0.637 15.9994 8 H1TRIS H20.463 1.0080 tel:2%C2%A0%C2%A0%C2%A0%200.463%C2%A0%C2%A0%201.0080 9 CH21TRIS C30.257 14.0270 10OA1TRIS O3 -0.637 15.9994 11 H1TRIS H30.463 1.0080 tel:3%C2%A0%C2%A0%C2%A0%200.463%C2%A0%C2%A0%201.0080 12 CH21TRIS C40.257 14.0270 13OA1TRIS O4 -0.636 15.9994 14 H1TRIS H40.463 1.0080 tel:4%C2%A0%C2%A0%C2%A0%200.463%C2%A0%C2%A0%201.0080 ; 1.000 ; total charge of the molecule: 1.000 -- Ahmet Yıldırım -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
