[gmx-users] Problem in setup energy minimization step(grompp)
Hi all, I am facing a problem when i tried the TIP4P water model for the set up of energy minimization using grompp. This error did'nt occur while using the spce model. Fatal error: number of coordinates in coordinate file (1.pdb, 31975) does not match topology (1.top, 24795) Please help me to rectify this problem. Thanks Bipin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Problem in setup energy minimization step(grompp)
Hi all, I am facing a problem when i tried the TIP4P water model for the set up of energy minimization using grompp. This error did'nt occur while using the spce model. Fatal error: number of coordinates in coordinate file (1.pdb, 31975) does not match topology (1.top, 24795) Please help me to rectify this problem. Thanks Bipin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Fatal error: No such moleculetype Cl
Hi, I am getting the following error. The ions.itp is included and I am using gromacs 4.0.5 with opls-aa and I included the Cl ion using genion. What am I doing wrong?? back Off! I just backed up mdout.mdp to ./#mdout.mdp.11# checking input for internal consistency... processing topology... Opening library file /opt/programs/gromacs/share/gromacs/top/ffoplsaa.itp Opening library file /opt/programs/gromacs/share/gromacs/top/ffoplsaanb.itp Opening library file /opt/programs/gromacs/share/gromacs/top/ffoplsaabon.itp Generated 332520 of the 332520 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 332520 of the 332520 1-4 parameter combinations Opening library file /opt/programs/gromacs/share/gromacs/top/spc.itp Opening library file /opt/programs/gromacs/share/gromacs/top/ions.itp Excluding 3 bonded neighbours molecule type 'Protein_A' Excluding 2 bonded neighbours molecule type 'SOL' --- Program grompp, VERSION 4.0.5 Source code file: toppush.c, line: 1641 Fatal error: No such moleculetype Cl --- _ The New Busy think 9 to 5 is a cute idea. Combine multiple calendars with Hotmail. http://www.windowslive.com/campaign/thenewbusy?tile=multicalendarocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_5-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Fatal error: No such moleculetype Cl
Okey, I found the solution, it is the IFDEF statements in ions.itp. OPLS does not have CL but a CL- and therefore when I changed to CL- in my $FILE.top, it went through smoothly. Cheers, From: xru...@live.com To: gmx-users@gromacs.org Date: Mon, 26 Jul 2010 06:58:57 + Subject: [gmx-users] Fatal error: No such moleculetype Cl Hi, I am getting the following error. The ions.itp is included and I am using gromacs 4.0.5 with opls-aa and I included the Cl ion using genion. What am I doing wrong?? back Off! I just backed up mdout.mdp to ./#mdout.mdp.11# checking input for internal consistency... processing topology... Opening library file /opt/programs/gromacs/share/gromacs/top/ffoplsaa.itp Opening library file /opt/programs/gromacs/share/gromacs/top/ffoplsaanb.itp Opening library file /opt/programs/gromacs/share/gromacs/top/ffoplsaabon.itp Generated 332520 of the 332520 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 332520 of the 332520 1-4 parameter combinations Opening library file /opt/programs/gromacs/share/gromacs/top/spc.itp Opening library file /opt/programs/gromacs/share/gromacs/top/ions.itp Excluding 3 bonded neighbours molecule type 'Protein_A' Excluding 2 bonded neighbours molecule type 'SOL' --- Program grompp, VERSION 4.0.5 Source code file: toppush.c, line: 1641 Fatal error: No such moleculetype Cl --- The New Busy think 9 to 5 is a cute idea. Combine multiple calendars with Hotmail. Get busy. _ Hotmail has tools for the New Busy. Search, chat and e-mail from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_1-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Problem in setup energy minimization step(grompp)
bipin.si...@research.iiit.ac.in wrote: Hi all, I am facing a problem when i tried the TIP4P water model for the set up of energy minimization using grompp. This error did'nt occur while using the spce model. Fatal error: number of coordinates in coordinate file (1.pdb, 31975) does not match topology (1.top, 24795) Please help me to rectify this problem. So all you did was change the water model? That would certainly explain it, since SPC/E is a 3-point model, and TIP4P has 4 sites. Otherwise: http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology -Justin Thanks Bipin -- 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Problem in setup energy minimization step(grompp)
Precisely, open your xyz.top file and search for #include spc.itp and replace this line with #include tip4p.itp and you will be done with. Date: Mon, 26 Jul 2010 07:00:57 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] Problem in setup energy minimization step(grompp) bipin.si...@research.iiit.ac.in wrote: Hi all, I am facing a problem when i tried the TIP4P water model for the set up of energy minimization using grompp. This error did'nt occur while using the spce model. Fatal error: number of coordinates in coordinate file (1.pdb, 31975) does not match topology (1.top, 24795) Please help me to rectify this problem. So all you did was change the water model? That would certainly explain it, since SPC/E is a 3-point model, and TIP4P has 4 sites. Otherwise: http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology -Justin Thanks Bipin -- 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ Hotmail is redefining busy with tools for the New Busy. Get more from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_2-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] decomposition
Hi Jacopo, from somewhere the information about the 7 nodes must have come. What are the exact commands you used? What MPI are you using? Carsten On Jul 26, 2010, at 12:35 PM, Jacopo Sgrignani wrote: Dear all i'm trying to run a MD simulation using domain decomposition but after two days i'm only able to get this error: There is no domain decomposition for 7 nodes that is compatible with the given box and a minimum cell size of 2.37175 nm Change the number of nodes or mdrun option -rcon or -dds or your LINCS settings Look in the log file for details on the domain decomposition I don't select a number of nodes but i use the default options, but the simulation does not run. So could you give me advices to run with domain decomp, or where can I find exaples about this? Thanks a lot Jacopo -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Problem in setup energy minimization step(grompp)
Date: Mon, 26 Jul 2010 07:26:04 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] Problem in setup energy minimization step(grompp) X Rules wrote: Precisely, open your xyz.top file and search for #include spc.itp and replace this line with #include tip4p.itp and you will be done with. Not if the coordinates present are for a three-point water model, in which case the same error is occurring. If you're switching models like this, you have to re-build the system. agreed, but I build my system entirely for tip4p, i.e adding tip4p using genbox and still my top file contains spc.itp instead of tip4p.itp (possible bug?? in 4.0.5 alteast). -Justin Date: Mon, 26 Jul 2010 07:00:57 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] Problem in setup energy minimization step(grompp) bipin.si...@research.iiit.ac.in wrote: Hi all, I am facing a problem when i tried the TIP4P water model for the set up of energy minimization using grompp. This error did'nt occur while using the spce model. Fatal error: number of coordinates in coordinate file (1.pdb, 31975) does not match topology (1.top, 24795) Please help me to rectify this problem. So all you did was change the water model? That would certainly explain it, since SPC/E is a 3-point model, and TIP4P has 4 sites. Otherwise: http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology -Justin Thanks Bipin -- 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php Hotmail is redefining busy with tools for the New Busy. Get more from your inbox. See how. http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_2 -- 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ Hotmail is redefining busy with tools for the New Busy. Get more from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_2-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Problem in setup energy minimization step(grompp)
X Rules wrote: Date: Mon, 26 Jul 2010 07:26:04 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] Problem in setup energy minimization step(grompp) X Rules wrote: Precisely, open your xyz.top file and search for #include spc.itp and replace this line with #include tip4p.itp and you will be done with. Not if the coordinates present are for a three-point water model, in which case the same error is occurring. If you're switching models like this, you have to re-build the system. agreed, but I build my system entirely for tip4p, i.e adding tip4p using genbox and still my top file contains spc.itp instead of tip4p.itp (possible bug?? in 4.0.5 alteast). There is no bug. The default water model written to the topology is spc.itp, but this can be chosen when running pdb2gmx with the -water flag. The mechanism for choosing water models will be completely different in the upcoming version of GROMACS, such that the choice will be completely user-dependent. -Justin -Justin Date: Mon, 26 Jul 2010 07:00:57 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] Problem in setup energy minimization step(grompp) bipin.si...@research.iiit.ac.in wrote: Hi all, I am facing a problem when i tried the TIP4P water model for the set up of energy minimization using grompp. This error did'nt occur while using the spce model. Fatal error: number of coordinates in coordinate file (1.pdb, 31975) does not match topology (1.top, 24795) Please help me to rectify this problem. So all you did was change the water model? That would certainly explain it, since SPC/E is a 3-point model, and TIP4P has 4 sites. Otherwise: http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology -Justin Thanks Bipin -- 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php Hotmail is redefining busy with tools for the New Busy. Get more from your inbox. See how. http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_2 -- 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php Hotmail is redefining busy with tools for the New Busy. Get more from your inbox. See how. http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_2 -- 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] nonbond_params
Hi, my system is composed of two molecules, each is composed of a 36 carbon like dummy atoms i defined in the amber files (i.e., has the LJ parameters of a carbon) I'm interested in eliminating the attractive Lennard-Jones interactions between the dummy atoms , such that only the repulsive terms will account. I thought of adding a section to the *.top file: [ nonbond params ] and to set c6 to 0 such that the attractive term of the LJ is eliminated. I used exactly the same syntax of the tutorial (page 98): * D D1 0.0E-00 0.34252E-05* ; (D is just the name of my dummy atom) but got a syntax error when running grompp: *Fatal error: Syntax error - File Surface_Surface_1.5_Sep_2.5.top, line 642 Last line read: '[ nonbond_params ]' Invalid order for directive nonbond_params* 1) what is wrong with my syntax? are there any further examples anywhere for the usage of [ nonbond params ] in topology files? 2) Is [ nonbond params ] the right strategy to the task i described? Many Thanks, Amir -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] nonbond_params
Amir Marcovitz wrote: Hi, my system is composed of two molecules, each is composed of a 36 carbon like dummy atoms i defined in the amber files (i.e., has the LJ parameters of a carbon) I'm interested in eliminating the attractive Lennard-Jones interactions between the dummy atoms , such that only the repulsive terms will account. I thought of adding a section to the *.top file: [ nonbond params ] and to set c6 to 0 such that the attractive term of the LJ is eliminated. I used exactly the same syntax of the tutorial (page 98): * D D1 0.0E-00 0.34252E-05* ; (D is just the name of my dummy atom) but got a syntax error when running grompp: *Fatal error: Syntax error - File Surface_Surface_1.5_Sep_2.5.top, line 642 Last line read: '[ nonbond_params ]' Invalid order for directive nonbond_params* 1) what is wrong with my syntax? are there any further examples anywhere for the usage of [ nonbond params ] in topology files? If you have already #included a force field file in the .top, it will have a [nonbond_params] section in it already. You cannot add a new one. The proper approach would be to modify the #included *nb.itp file. 2) Is [ nonbond params ] the right strategy to the task i described? Sounds like one way to do it. -Justin Many Thanks, Amir -- 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] energies in amber, namd and gromacs
Hi there, I have a very simple case of a tri alanine (AAA). You can use tleap to create such peptide and save the pdb and amber's parameters. Then I do a single point calculation to get the potential energy. I am using mdin like: cat EOF | mdin Single point cntrl imin=0, maxcyc=0, ntmin=2, ntb=0, igb=0, cut=999, / EOF Then I test the same input parameters with Namd2, using namd.conf: cat EOF | AAAamb_namd.conf outputEnergies 1 # Energy output frequency DCDfreq1 # Trajectory file frequency timestep 2 # in unit of fs temperature300 # Initial temp for velocity assignment cutoff 999 switching off # Turn off the switching functions PMEoff # Use PME for electrostatic calculation amber on # Specify this is AMBER force field parmfile AAAamb.prmtop # Input PARM file ambercoor AAAamb.inpcrd # Input coordinate file outputname AAAamb # Prefix of output files excludescaled1-4 1-4scaling 0.83 # =1/1.2, default is 1.0 minimize 0 EOF I have only a 0.001 kcal/mol absolute diff (or relative 0.0037%) for the Elec term, everything else is absolutely the same. Then comes gromacs. I convert my prmtop and inpcrd to gromcs top and gro with either acpype or amb2gmx and then doing a single point with file: cat EOF | SPE.mdp integrator = md nsteps = 0 dt = 0.001 constraints = none emtol= 10.0 emstep = 0.01 nstcomm = 1 ns_type = simple nstlist = 0 rlist= 0 rcoulomb = 0 rvdw = 0 Tcoupl = no Pcoupl = no gen_vel = no nstxout = 1 pbc = no nstlog = 1 nstenergy = 1 nstvout = 1 nstfout = 1 nstxtcout = 1 comm_mode = ANGULAR EOF Converting gromacs energies (kJ/mol) by dividing the terms by 4.184 and they don't match amber/namd results. See relative diffs (abs(g-a)/max(abs(a),abs(g))): Bond:5.87% Angle: 3.49% Dihe:0.14% vdW: 0.52% Elec:0.17% Pot.Tot: 5.90% I am very surprised to find this difference, in special for Bond since it's for this term essentially the same equation and parameters. Any ideas of what could be missing here? Many thanks, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] nonbond_params
Thank you Justin, I didn't understand though where can I edit the [ nonbond params ] section? Is there a better way to define pairs with no LJ attraction that will ignore the settings in the *nb.itp file? Cheers, Amir On Mon, Jul 26, 2010 at 5:31 PM, Justin A. Lemkul jalem...@vt.edu wrote: Amir Marcovitz wrote: Hi, my system is composed of two molecules, each is composed of a 36 carbon like dummy atoms i defined in the amber files (i.e., has the LJ parameters of a carbon) I'm interested in eliminating the attractive Lennard-Jones interactions between the dummy atoms , such that only the repulsive terms will account. I thought of adding a section to the *.top file: [ nonbond params ] and to set c6 to 0 such that the attractive term of the LJ is eliminated. I used exactly the same syntax of the tutorial (page 98): * D D1 0.0E-00 0.34252E-05* ; (D is just the name of my dummy atom) but got a syntax error when running grompp: *Fatal error: Syntax error - File Surface_Surface_1.5_Sep_2.5.top, line 642 Last line read: '[ nonbond_params ]' Invalid order for directive nonbond_params* 1) what is wrong with my syntax? are there any further examples anywhere for the usage of [ nonbond params ] in topology files? If you have already #included a force field file in the .top, it will have a [nonbond_params] section in it already. You cannot add a new one. The proper approach would be to modify the #included *nb.itp file. 2) Is [ nonbond params ] the right strategy to the task i described? Sounds like one way to do it. -Justin Many Thanks, Amir -- 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] nonbond_params
The [ nonbond_params ] section is located in the nb.itp file of your chosen force field. The error comes from the fact that you have likely tried to introduce an additional [ nonbond_params ] directive within your .top file, which is incorrect. You cannot have multiple entries for these directives, and they must follow a certain order (given somewhere in the manual). To introduce the additional atom type, you'll need to edit the nb.itp and .atp file for your force field to account for the new atom type. -Justin Amir Marcovitz wrote: Thank you Justin, I didn't understand though where can I edit the [ nonbond params ] section? Is there a better way to define pairs with no LJ attraction that will ignore the settings in the *nb.itp file? Cheers, Amir On Mon, Jul 26, 2010 at 5:31 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Amir Marcovitz wrote: Hi, my system is composed of two molecules, each is composed of a 36 carbon like dummy atoms i defined in the amber files (i.e., has the LJ parameters of a carbon) I'm interested in eliminating the attractive Lennard-Jones interactions between the dummy atoms , such that only the repulsive terms will account. I thought of adding a section to the *.top file: [ nonbond params ] and to set c6 to 0 such that the attractive term of the LJ is eliminated. I used exactly the same syntax of the tutorial (page 98): * D D1 0.0E-00 0.34252E-05* ; (D is just the name of my dummy atom) but got a syntax error when running grompp: *Fatal error: Syntax error - File Surface_Surface_1.5_Sep_2.5.top, line 642 Last line read: '[ nonbond_params ]' Invalid order for directive nonbond_params* 1) what is wrong with my syntax? are there any further examples anywhere for the usage of [ nonbond params ] in topology files? If you have already #included a force field file in the .top, it will have a [nonbond_params] section in it already. You cannot add a new one. The proper approach would be to modify the #included *nb.itp file. 2) Is [ nonbond params ] the right strategy to the task i described? Sounds like one way to do it. -Justin Many Thanks, Amir -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Errors with g_dielectric
Hello, I am trying to calculate the dielectric constant for pure tetrahydrofuran (THF) at 298K. I keep running into problems though. I have looked through the gmx user list to see if others have had these problems, but I didn't see any mention of them (although I did see that others were asked to report issues with g_dipoles to bugzilla). The first thing I do is run g_dipoles using the command (I do this in order to get the ACF to use in g_dielectric): g_dipoles -f nvt10ns.xtc -s previous.tpr -corr mol -mu 1.75 *I would have liked to attach the tpr and xtc file, but the message was too big. I can send them if they will help* When I do this, I get the following output to terminal: There are 255 molecules in the selection Using volume from topology: 34.3361 nm^3 Last Frame 3 time 12000.001 t0 0, t 12000, teller 30001 **then there is a long pause (approx 5 minutes)** Dipole Moment (Debye) __ Average = 1.9194 Std. Dev. = 0.0085 Error = 0. **Then it lists the different dipole moments, kirkwood factors, and finally an epsilon = 4.47756** (I cannot attach the output files since they too make this e-mail too big. I will send them if requested.) It seems that the g_dipoles is working fine for me. Once I have the autocorrelation function (dipcorr.xvg), I want to use g_dielectric. Before I talk about the problems I have here, I wanted to verify a few things about the various options: epsRF - the default here is 78.5, even though the default in g_dipoles is 0 (infinity). I wanted it to be infinity, so I assume I change it. eps0 - this is the epsilon of my liquid - but is it the epsilon that was calculated from g_dipoles (4.47756)? When I run the command: g_dielectric -f dipcorr.xvg -epsRF 0 -d -o -c I get a segmentation fault before anything happens: Read data set containing 2 columns and 15001 rows Assuming (from data) that timestep is 0.4, nxtail = 1249 Creating standard deviation numbers ... nbegin = 13, x[nbegin] = 5.2, tbegin = 5 Segmentation Fault If I leave out the -epsRF, I still get the same error. If I include eps0, I still get a segmentation fault. It seems strange to me since GROMACS generates the input and yet has an issue with it. I would like to point out that the manual states to use dipcorr.xvg to get the dielectric constant, but after reading the paper GROMACS references, it seems that Mtot^2 is more appropriate. I tried running the command g_dielectric -f Mtot.xvg, and the segmentation fault went away. Instead lambda went to infinity and there was a fatal error (nparm = 0 in the file ../../../../src/tools/exptfit. c, line 466. I am probably missing something obvious, but I am having a hard time figuring out what it is. I appreciate any help. Thank you for your time, Jenny -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Ryckaert Bellemanm-dihedral in OPLS-AA
Thank you dear justin... I will go through the primary literature of oplsaa forcefield... -- *SUMANTH KUMAR.M* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
