Re: [gmx-users] [ defaults ] and nonbonded
Whether it would be that easy i will find it. I specified my own potential (not LJ) - so how come I should choose option 1 or 2 in nbfunct? I changed h(x) in my table 6th column. On Wed, Jun 12, 2013 at 1:18 AM, Justin Lemkul jalem...@vt.edu wrote: On 6/11/13 4:12 PM, Steven Neumann wrote: Dear Gromacs Users, I got really confused: In manual [defualts ]: nbfunc is the non-bonded function type. Use 1 (Lennard-Jones) or 2 (Buckingham) I want to use mdrun -table table.xvg with my own potential, which one I should choose? gen-pairs - is for pair generation. The default is ‘no’, i.e. get 1-4 parameters from the pairtypes list. When parameters are not present in the list, stop with a fatal error. Setting‘yes’ generates 1-4 parameters that are not present in the pair list from normal Lennard-Jones parameters using fudgeLJ I want to have all intramolecular atoms (within my chain) interacting (no exclusions) with each other from [ atomtypes ] in ffnonbonded.itp Does it mean yes with nrexcl =1 in my topology? And sth I also got confused: [ pairtypes ] are only 1-4 parameters or here I can specify parameters for all atoms within my molecule? So [ atomtypes ] in ffnonbonded.itp also correspond to intra molecular interactions? These topics are discussed frequently. Please search the archive; surely you will find relevant topics. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist 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 -- 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] Tutor directory in gromacs 4.6
Hope I'm not missing something obvious here - but I can't find the 'share/tutor' directory in my Gromacs 4.6 installation. Should it be there ? thanks, Colin -- View this message in context: http://gromacs.5086.x6.nabble.com/Tutor-directory-in-gromacs-4-6-tp5009078.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] dssp works fine, but do_dssp gives fatal error
Dear all, I installed dssp (Version 2.0.4) and it works perfect on a .pdb file. I am trying to use it for do_dssp command but get the following error each time: Fatal error: Failed to execute command: /usr/local/bin/dssp -na ddtmi68v ddwLuK68 /dev/null 2 /dev/null Is there any way to rectify it? Thanks. Nikunj -- 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] Tutor directory in gromacs 4.6
There are no such directory. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Wed, Jun 12, 2013 at 1:56 PM, colinbannister colin.bannis...@nottingham.ac.uk wrote: Hope I'm not missing something obvious here - but I can't find the 'share/tutor' directory in my Gromacs 4.6 installation. Should it be there ? thanks, Colin -- View this message in context: http://gromacs.5086.x6.nabble.com/Tutor-directory-in-gromacs-4-6-tp5009078.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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 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] dssp works fine, but do_dssp gives fatal error
Hi, Search the mailing list. This problem and its solution has been repeatedly discussed. Erik On 12 Jun 2013, at 10:31, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Dear all, I installed dssp (Version 2.0.4) and it works perfect on a .pdb file. I am trying to use it for do_dssp command but get the following error each time: Fatal error: Failed to execute command: /usr/local/bin/dssp -na ddtmi68v ddwLuK68 /dev/null 2 /dev/null Is there any way to rectify it? Thanks. Nikunj -- 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 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] Tutor directory in gromacs 4.6
Chandan, I was looking at : http://manual.gromacs.org/online/getting_started.html#setup Which mentions these files. Is this wrong ? thanks, Colin -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Chandan Choudhury Sent: 12 June 2013 09:32 To: Discussion list for GROMACS users Subject: Re: [gmx-users] Tutor directory in gromacs 4.6 There are no such directory. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Wed, Jun 12, 2013 at 1:56 PM, colinbannister colin.bannis...@nottingham.ac.uk wrote: Hope I'm not missing something obvious here - but I can't find the 'share/tutor' directory in my Gromacs 4.6 installation. Should it be there ? thanks, Colin -- View this message in context: http://gromacs.5086.x6.nabble.com/Tutor-directory-in-gromacs-4-6-tp500 9078.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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 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 This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system, you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation. -- 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] dssp works fine, but do_dssp gives fatal error
Yes I did searched. But for most people, there were issues regarding the path or wrong DSSP. DSSP runs for me, but do_dssp does not. On Wed, Jun 12, 2013 at 2:25 PM, Erik Marklund er...@xray.bmc.uu.se wrote: Hi, Search the mailing list. This problem and its solution has been repeatedly discussed. Erik On 12 Jun 2013, at 10:31, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Dear all, I installed dssp (Version 2.0.4) and it works perfect on a .pdb file. I am trying to use it for do_dssp command but get the following error each time: Fatal error: Failed to execute command: /usr/local/bin/dssp -na ddtmi68v ddwLuK68 /dev/null 2 /dev/null Is there any way to rectify it? Thanks. Nikunj -- 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 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 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] Issues with energy when running in the microcanonical ensemble
Dear all, I'm using Gromacs 4.5.5 with the amber ff99SB forcefield to run NVE simulations on ethane in 725 TIP3P water molecules. I used antechamber to parametrise my ethane. I have 2 issues; Firstly the energy conservation of my simulations seems to get worse as I lower my timestep, here is an example .mdp file that I'm using: integrator = md-vv gen_vel = no nsteps = 100 dt = 0.001 nstlist = 10 rlist = 1.3 coulombtype = pme rcoulomb= 1.0 vdw-type= Shift rvdw= 1.0 tcoupl = no pcoupl = no nstenergy = 100 I found a link describing that it could be an issue with the precision and that Gromacs can be installed with double precision: http://www.gromacs.org/Documentation/Terminology/Conserving_Energy but is this the only way to ensure energy conservation? My second issue is with the calculation of the kinetic energy, I have 2183 atoms in my simulation box which means the kinetic energy should be (roughly) 0.5 * 3*2183-3(degrees of freedom) * 0.001987204118(kB) * 300(T) * 4.184(conversion from kcal/mol to kJ/mol) = 8163.97 however, when I look in my simulation the kinetic energy Gromacs outputs is 5498.20 Step Time Lambda 00.00.0 Energies (kJ/mol) Bond Angle Ryckaert-Bell. LJ-14 Coulomb-14 5.95743e+001.96046e+014.71247e-015.73520e-013.92661e+00 LJ (SR) Coulomb (SR) Coul. recip. PotentialKinetic En. 5.12842e+03 -3.20604e+04 -2.67111e+03 -2.95726e+045.49820e+03 Total EnergyTemperature Pressure (bar) -2.40744e+043.02575e+02 -1.82251e+03 By running in NVE I'm not using a thermostat and can't find any reason in the manual to scale the kinetic energy. Is there an a reason I'm missing as to why my kinetic energy seems lower than it should be? Best Wishes Chris -- 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] Nonbonded parameters
Dear Gmx Users, Please, correct me if I am wrong. In ffnonbonded.itp [ atomtypes ] - these are nonbonded parameters between atoms of the same type [ nonbond_params ] these are nonbonded parameters between atoms of different type [ pairtypes ] - 1-4 interactions If that is correct why amber force filed has only [atomtypes] column? How nonbonded parameters are calculated between atoms of a different type? The same with charmm - only [atomtypes ] and [pairtypes ] are provided. Would you please explain? Steven -- 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: distance_restraints
On 6/12/13 12:10 AM, maggin wrote: Hi, Justin, You are right, I should first fix the bad geometry. I check 1dx0.pdb, and the problematic areas are: atom1 atom2 1 N1+ (GLY124 N) 4 H (GLY124 HT3) 181 C (PRO137 CD)182 H (PRO137 HD1) 262 H (PHE141 HD1) 263 C (PHE141 CE2) 296 O1-(ASP144 OD2) 297 C (ASP144 C) 685 O (PRO165 O) 688 C (VAL166 CA) for these atoms bonds that rotated more than 30 degrees 1dx0.pdb is get from NMR. So, for the initial structure , is there anyways to solve these LINCS WARNING ? What does visual inspection tell you about these areas: (1) from the NMR structure and (2) after steep minimization? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] Tutor directory in gromacs 4.6
On 6/12/13 4:52 AM, Colin Bannister wrote: Chandan, I was looking at : http://manual.gromacs.org/online/getting_started.html#setup Which mentions these files. Is this wrong ? Yes, it is. Several pages in the online manual are outdated, and share/tutor was removed some time ago because it was agreed that these examples were less than useful. Refer to http://www.gromacs.org/Documentation/Tutorials for far more detailed tutorials. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] Nonbonded parameters
On 6/12/13 5:30 AM, Steven Neumann wrote: Dear Gmx Users, Please, correct me if I am wrong. In ffnonbonded.itp [ atomtypes ] - these are nonbonded parameters between atoms of the same type No, these are the nonbonded parameters that are used when applying combination rules between any atoms. [ nonbond_params ] these are nonbonded parameters between atoms of different type No, these override combination rules. [ pairtypes ] - 1-4 interactions If that is correct why amber force filed has only [atomtypes] column? How nonbonded parameters are calculated between atoms of a different type? The same with charmm - only [atomtypes ] and [pairtypes ] are provided. Would you please explain? Gromos force fields, for instance, have complex ways of generating nonbonded interactions that are not always the same for a given atomtype. Other force fields just use straight combination rules and thus never need [nonbond_params]. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] Nonbonded parameters
Thank you. That means that e.g. when two LJ atoms of a different type approaching each other the non bonded LJ potential energy is a sum of two potentials of those atoms? On Wed, Jun 12, 2013 at 10:44 AM, Justin Lemkul jalem...@vt.edu wrote: On 6/12/13 5:30 AM, Steven Neumann wrote: Dear Gmx Users, Please, correct me if I am wrong. In ffnonbonded.itp [ atomtypes ] - these are nonbonded parameters between atoms of the same type No, these are the nonbonded parameters that are used when applying combination rules between any atoms. [ nonbond_params ] these are nonbonded parameters between atoms of different type No, these override combination rules. [ pairtypes ] - 1-4 interactions If that is correct why amber force filed has only [atomtypes] column? How nonbonded parameters are calculated between atoms of a different type? The same with charmm - only [atomtypes ] and [pairtypes ] are provided. Would you please explain? Gromos force fields, for instance, have complex ways of generating nonbonded interactions that are not always the same for a given atomtype. Other force fields just use straight combination rules and thus never need [nonbond_params]. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist 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 -- 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] Nonbonded parameters
On 6/12/13 6:00 AM, Steven Neumann wrote: Thank you. That means that e.g. when two LJ atoms of a different type approaching each other the non bonded LJ potential energy is a sum of two potentials of those atoms? No, please refer to the Gromacs manual for discussion on combination rules and how they fit into the Lennard-Jones equation. -Justin On Wed, Jun 12, 2013 at 10:44 AM, Justin Lemkul jalem...@vt.edu wrote: On 6/12/13 5:30 AM, Steven Neumann wrote: Dear Gmx Users, Please, correct me if I am wrong. In ffnonbonded.itp [ atomtypes ] - these are nonbonded parameters between atoms of the same type No, these are the nonbonded parameters that are used when applying combination rules between any atoms. [ nonbond_params ] these are nonbonded parameters between atoms of different type No, these override combination rules. [ pairtypes ] - 1-4 interactions If that is correct why amber force filed has only [atomtypes] column? How nonbonded parameters are calculated between atoms of a different type? The same with charmm - only [atomtypes ] and [pairtypes ] are provided. Would you please explain? Gromos force fields, for instance, have complex ways of generating nonbonded interactions that are not always the same for a given atomtype. Other force fields just use straight combination rules and thus never need [nonbond_params]. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist 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 -- Justin A. Lemkul, Ph.D. Research Scientist 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
Fw: Aw: [gmx-users] Enthalpy Confusion
I appologise with the below, I got entropy and enthalpy confused for a mement. Funny. Stephan Gesendet:Dienstag, 11. Juni 2013 um 23:54 Uhr Von:lloyd riggs lloyd.ri...@gmx.ch An:Discussion list for GROMACS users gmx-users@gromacs.org Betreff:Aw: [gmx-users] Enthalpy Confusion If you only want the total for the system or a delta for an entire run, indexed group there of, covarience (covar/aneig) does a good job. I found neither actually fit, but the covarience does, or if you do it by hand using only LJ parmeters for the indexed sets, however I was using proteins, so for the fluid system ?, but it took some publication look ups that were quite old. (well not that old 1980s) Stephan Gesendet:Dienstag, 11. Juni 2013 um 20:09 Uhr Von:Jeffery Perkins jeffery.perk...@ufv.ca An:gmx-users@gromacs.org Betreff:[gmx-users] Enthalpy Confusion This may just be me not understanding what Im looking at, but Im trying to get the Enthalpy of a simple test system of LJ fluid, running version 4.5.4 initially Ive tried using the enthalpy option in g_energy but I noticed that if i compare that value to H=U+pV using either the average or the instantaneous values from g_energy switched over to SI so that there is no issue there, the results are different (manual calculation is around 2x the g_energy result). So the question is, what am I overlooking in the analysis of the data i have? -- View this message in context: http://gromacs.5086.x6.nabble.com/Enthalpy-Confusion-tp5009053.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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 dont post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Cant 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] Nonbonded parameters
On Wed, Jun 12, 2013 at 11:05 AM, Justin Lemkul jalem...@vt.edu wrote: On 6/12/13 6:00 AM, Steven Neumann wrote: Thank you. That means that e.g. when two LJ atoms of a different type approaching each other the non bonded LJ potential energy is a sum of two potentials of those atoms? No, please refer to the Gromacs manual for discussion on combination rules and how they fit into the Lennard-Jones equation. -Justin I read it. I used combination rule 1 in which C=4epsSig^6 and A=4epsSig^12 - So that means that when you provide in [atomtypes] in ffnonbonded your C and A values each atom has a specific LJ potential shape. Right? So two of them approaching each other in my system will have have the sum of it. Steven On Wed, Jun 12, 2013 at 10:44 AM, Justin Lemkul jalem...@vt.edu wrote: On 6/12/13 5:30 AM, Steven Neumann wrote: Dear Gmx Users, Please, correct me if I am wrong. In ffnonbonded.itp [ atomtypes ] - these are nonbonded parameters between atoms of the same type No, these are the nonbonded parameters that are used when applying combination rules between any atoms. [ nonbond_params ] these are nonbonded parameters between atoms of different type No, these override combination rules. [ pairtypes ] - 1-4 interactions If that is correct why amber force filed has only [atomtypes] column? How nonbonded parameters are calculated between atoms of a different type? The same with charmm - only [atomtypes ] and [pairtypes ] are provided. Would you please explain? Gromos force fields, for instance, have complex ways of generating nonbonded interactions that are not always the same for a given atomtype. Other force fields just use straight combination rules and thus never need [nonbond_params]. -Justin -- ==== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin h**ttp://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 htt**p://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/Searchh**ttp://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 http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==**== Justin A. Lemkul, Ph.D. Research Scientist 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 -- 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] dssp works fine, but do_dssp gives fatal error
Right. And what is its location? On Jun 12, 2013 11:17 AM, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Yes I did searched. But for most people, there were issues regarding the path or wrong DSSP. DSSP runs for me, but do_dssp does not. On Wed, Jun 12, 2013 at 2:25 PM, Erik Marklund er...@xray.bmc.uu.se wrote: Hi, Search the mailing list. This problem and its solution has been repeatedly discussed. Erik On 12 Jun 2013, at 10:31, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Dear all, I installed dssp (Version 2.0.4) and it works perfect on a .pdb file. I am trying to use it for do_dssp command but get the following error each time: Fatal error: Failed to execute command: /usr/local/bin/dssp -na ddtmi68v ddwLuK68 /dev/null 2 /dev/null Is there any way to rectify it? Thanks. Nikunj -- 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 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 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 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] [ defaults ] and nonbonded
You've got a test case that shows your tables do what you think they do, right? I would vary this setting and expect to see no effect. Mark On Jun 12, 2013 10:03 AM, Steven Neumann s.neuman...@gmail.com wrote: Whether it would be that easy i will find it. I specified my own potential (not LJ) - so how come I should choose option 1 or 2 in nbfunct? I changed h(x) in my table 6th column. On Wed, Jun 12, 2013 at 1:18 AM, Justin Lemkul jalem...@vt.edu wrote: On 6/11/13 4:12 PM, Steven Neumann wrote: Dear Gromacs Users, I got really confused: In manual [defualts ]: nbfunc is the non-bonded function type. Use 1 (Lennard-Jones) or 2 (Buckingham) I want to use mdrun -table table.xvg with my own potential, which one I should choose? gen-pairs - is for pair generation. The default is ‘no’, i.e. get 1-4 parameters from the pairtypes list. When parameters are not present in the list, stop with a fatal error. Setting‘yes’ generates 1-4 parameters that are not present in the pair list from normal Lennard-Jones parameters using fudgeLJ I want to have all intramolecular atoms (within my chain) interacting (no exclusions) with each other from [ atomtypes ] in ffnonbonded.itp Does it mean yes with nrexcl =1 in my topology? And sth I also got confused: [ pairtypes ] are only 1-4 parameters or here I can specify parameters for all atoms within my molecule? So [ atomtypes ] in ffnonbonded.itp also correspond to intra molecular interactions? These topics are discussed frequently. Please search the archive; surely you will find relevant topics. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search http://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_Lists 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 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] dssp works fine, but do_dssp gives fatal error
The location of dssp is /usr/local/bin/dssp On Wed, Jun 12, 2013 at 3:43 PM, Mark Abraham mark.j.abra...@gmail.comwrote: Right. And what is its location? On Jun 12, 2013 11:17 AM, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Yes I did searched. But for most people, there were issues regarding the path or wrong DSSP. DSSP runs for me, but do_dssp does not. On Wed, Jun 12, 2013 at 2:25 PM, Erik Marklund er...@xray.bmc.uu.se wrote: Hi, Search the mailing list. This problem and its solution has been repeatedly discussed. Erik On 12 Jun 2013, at 10:31, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Dear all, I installed dssp (Version 2.0.4) and it works perfect on a .pdb file. I am trying to use it for do_dssp command but get the following error each time: Fatal error: Failed to execute command: /usr/local/bin/dssp -na ddtmi68v ddwLuK68 /dev/null 2 /dev/null Is there any way to rectify it? Thanks. Nikunj -- 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 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 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 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 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] Nonbonded parameters
I got it. However, I have 60 atoms in my chain all with given C6 and C12 with a combination rule 1. When running grompp: Generated 1830 of the 1830 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 1830 of the 1830 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_X' Analysing residue names: There are: 1Protein residues Analysing Protein... Number of degrees of freedom in T-Coupling group rest is 118.00 This run will generate roughly 2 Mb of data when changing nrexcl in my topology to 0: Generated 1830 of the 1830 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 1830 of the 1830 1-4 parameter combinations Excluding 0 bonded neighbours molecule type 'Protein_chain_X' Analysing residue names: There are: 1Protein residues Analysing Protein... Number of degrees of freedom in T-Coupling group rest is 118.00 This run will generate roughly 2 Mb of data So if I exclude 1-3 interactions I have the same number of nonbonded parameters as well as 1-4 interactions. Can someone explain me this please? On Wed, Jun 12, 2013 at 11:12 AM, Steven Neumann s.neuman...@gmail.comwrote: On Wed, Jun 12, 2013 at 11:05 AM, Justin Lemkul jalem...@vt.edu wrote: On 6/12/13 6:00 AM, Steven Neumann wrote: Thank you. That means that e.g. when two LJ atoms of a different type approaching each other the non bonded LJ potential energy is a sum of two potentials of those atoms? No, please refer to the Gromacs manual for discussion on combination rules and how they fit into the Lennard-Jones equation. -Justin I read it. I used combination rule 1 in which C=4epsSig^6 and A=4epsSig^12 - So that means that when you provide in [atomtypes] in ffnonbonded your C and A values each atom has a specific LJ potential shape. Right? So two of them approaching each other in my system will have have the sum of it. Steven On Wed, Jun 12, 2013 at 10:44 AM, Justin Lemkul jalem...@vt.edu wrote: On 6/12/13 5:30 AM, Steven Neumann wrote: Dear Gmx Users, Please, correct me if I am wrong. In ffnonbonded.itp [ atomtypes ] - these are nonbonded parameters between atoms of the same type No, these are the nonbonded parameters that are used when applying combination rules between any atoms. [ nonbond_params ] these are nonbonded parameters between atoms of different type No, these override combination rules. [ pairtypes ] - 1-4 interactions If that is correct why amber force filed has only [atomtypes] column? How nonbonded parameters are calculated between atoms of a different type? The same with charmm - only [atomtypes ] and [pairtypes ] are provided. Would you please explain? Gromos force fields, for instance, have complex ways of generating nonbonded interactions that are not always the same for a given atomtype. Other force fields just use straight combination rules and thus never need [nonbond_params]. -Justin -- ==== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin h**ttp://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 htt**p://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/Searchh**ttp://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 http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==**== Justin A. Lemkul, Ph.D. Research Scientist 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
Re: [gmx-users] dssp works fine, but do_dssp gives fatal error
Search again. The syntax for invoking dssp changed at some point and it took a while before do_dssp adapted to that. If your do_dssp is lacking the -ver option then I'm quite confident that it uses the old syntax, which doesn't work with the newer versions (v. 2.0+ I think) of dssp. Erik On 12 Jun 2013, at 11:17, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Yes I did searched. But for most people, there were issues regarding the path or wrong DSSP. DSSP runs for me, but do_dssp does not. On Wed, Jun 12, 2013 at 2:25 PM, Erik Marklund er...@xray.bmc.uu.se wrote: Hi, Search the mailing list. This problem and its solution has been repeatedly discussed. Erik On 12 Jun 2013, at 10:31, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Dear all, I installed dssp (Version 2.0.4) and it works perfect on a .pdb file. I am trying to use it for do_dssp command but get the following error each time: Fatal error: Failed to execute command: /usr/local/bin/dssp -na ddtmi68v ddwLuK68 /dev/null 2 /dev/null Is there any way to rectify it? Thanks. Nikunj -- 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 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 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 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] dssp works fine, but do_dssp gives fatal error
Yes I checked. do_dssp has no -ver option. I also found out this link https://gerrit.gromacs.org/#/c/687/ but dont know how to install/use it. Or maybe I can install DsspOld and see? On Wed, Jun 12, 2013 at 4:15 PM, Erik Marklund er...@xray.bmc.uu.se wrote: Search again. The syntax for invoking dssp changed at some point and it took a while before do_dssp adapted to that. If your do_dssp is lacking the -ver option then I'm quite confident that it uses the old syntax, which doesn't work with the newer versions (v. 2.0+ I think) of dssp. Erik On 12 Jun 2013, at 11:17, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Yes I did searched. But for most people, there were issues regarding the path or wrong DSSP. DSSP runs for me, but do_dssp does not. On Wed, Jun 12, 2013 at 2:25 PM, Erik Marklund er...@xray.bmc.uu.se wrote: Hi, Search the mailing list. This problem and its solution has been repeatedly discussed. Erik On 12 Jun 2013, at 10:31, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Dear all, I installed dssp (Version 2.0.4) and it works perfect on a .pdb file. I am trying to use it for do_dssp command but get the following error each time: Fatal error: Failed to execute command: /usr/local/bin/dssp -na ddtmi68v ddwLuK68 /dev/null 2 /dev/null Is there any way to rectify it? Thanks. Nikunj -- 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 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 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 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 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] dssp works fine, but do_dssp gives fatal error
You have (at least) two easy options. 1) Install old_dssp that is available through the dssp web page. 2) Install a newer version of gromacs than you have at the moment. What version do you currently use? Erik On 12 Jun 2013, at 12:56, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Yes I checked. do_dssp has no -ver option. I also found out this link https://gerrit.gromacs.org/#/c/687/ but dont know how to install/use it. Or maybe I can install DsspOld and see? On Wed, Jun 12, 2013 at 4:15 PM, Erik Marklund er...@xray.bmc.uu.se wrote: Search again. The syntax for invoking dssp changed at some point and it took a while before do_dssp adapted to that. If your do_dssp is lacking the -ver option then I'm quite confident that it uses the old syntax, which doesn't work with the newer versions (v. 2.0+ I think) of dssp. Erik On 12 Jun 2013, at 11:17, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Yes I did searched. But for most people, there were issues regarding the path or wrong DSSP. DSSP runs for me, but do_dssp does not. On Wed, Jun 12, 2013 at 2:25 PM, Erik Marklund er...@xray.bmc.uu.se wrote: Hi, Search the mailing list. This problem and its solution has been repeatedly discussed. Erik On 12 Jun 2013, at 10:31, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Dear all, I installed dssp (Version 2.0.4) and it works perfect on a .pdb file. I am trying to use it for do_dssp command but get the following error each time: Fatal error: Failed to execute command: /usr/local/bin/dssp -na ddtmi68v ddwLuK68 /dev/null 2 /dev/null Is there any way to rectify it? Thanks. Nikunj -- 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 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 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 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 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 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] dssp works fine, but do_dssp gives fatal error
My current Gromacs version is 4.5.5 I think using the first option will be easy and quick. On Wed, Jun 12, 2013 at 4:41 PM, Erik Marklund er...@xray.bmc.uu.se wrote: You have (at least) two easy options. 1) Install old_dssp that is available through the dssp web page. 2) Install a newer version of gromacs than you have at the moment. What version do you currently use? Erik On 12 Jun 2013, at 12:56, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Yes I checked. do_dssp has no -ver option. I also found out this link https://gerrit.gromacs.org/#/c/687/ but dont know how to install/use it. Or maybe I can install DsspOld and see? On Wed, Jun 12, 2013 at 4:15 PM, Erik Marklund er...@xray.bmc.uu.se wrote: Search again. The syntax for invoking dssp changed at some point and it took a while before do_dssp adapted to that. If your do_dssp is lacking the -ver option then I'm quite confident that it uses the old syntax, which doesn't work with the newer versions (v. 2.0+ I think) of dssp. Erik On 12 Jun 2013, at 11:17, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Yes I did searched. But for most people, there were issues regarding the path or wrong DSSP. DSSP runs for me, but do_dssp does not. On Wed, Jun 12, 2013 at 2:25 PM, Erik Marklund er...@xray.bmc.uu.se wrote: Hi, Search the mailing list. This problem and its solution has been repeatedly discussed. Erik On 12 Jun 2013, at 10:31, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: Dear all, I installed dssp (Version 2.0.4) and it works perfect on a .pdb file. I am trying to use it for do_dssp command but get the following error each time: Fatal error: Failed to execute command: /usr/local/bin/dssp -na ddtmi68v ddwLuK68 /dev/null 2 /dev/null Is there any way to rectify it? Thanks. Nikunj -- 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 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 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 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 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 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 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] Umbrella Sampling Force component output
Dear Gromacs Users, I runned and Umbrella Sampling simulation but I made a mistake in the value of the pull_dim option, so gromacs printed the z component of the force instead of the x component that i need (with the option -pf of mdrun). I have all files from the simulation. Is there a way to get the x component of the force without running the simulation again? Thanks in advanced, Kenny -- 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] Nonbonded parameters
An why do I have 1830 non bonded? 60*60/2 = 1800. There are 57 of 1-4 combinations so it should be lower than 1800... And why 1830 1-4 interactions as I have only 57... Please, help/ Steven On Wed, Jun 12, 2013 at 11:40 AM, Steven Neumann s.neuman...@gmail.comwrote: I got it. However, I have 60 atoms in my chain all with given C6 and C12 with a combination rule 1. When running grompp: Generated 1830 of the 1830 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 1830 of the 1830 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_X' Analysing residue names: There are: 1Protein residues Analysing Protein... Number of degrees of freedom in T-Coupling group rest is 118.00 This run will generate roughly 2 Mb of data when changing nrexcl in my topology to 0: Generated 1830 of the 1830 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 1830 of the 1830 1-4 parameter combinations Excluding 0 bonded neighbours molecule type 'Protein_chain_X' Analysing residue names: There are: 1Protein residues Analysing Protein... Number of degrees of freedom in T-Coupling group rest is 118.00 This run will generate roughly 2 Mb of data So if I exclude 1-3 interactions I have the same number of nonbonded parameters as well as 1-4 interactions. Can someone explain me this please? On Wed, Jun 12, 2013 at 11:12 AM, Steven Neumann s.neuman...@gmail.comwrote: On Wed, Jun 12, 2013 at 11:05 AM, Justin Lemkul jalem...@vt.edu wrote: On 6/12/13 6:00 AM, Steven Neumann wrote: Thank you. That means that e.g. when two LJ atoms of a different type approaching each other the non bonded LJ potential energy is a sum of two potentials of those atoms? No, please refer to the Gromacs manual for discussion on combination rules and how they fit into the Lennard-Jones equation. -Justin I read it. I used combination rule 1 in which C=4epsSig^6 and A=4epsSig^12 - So that means that when you provide in [atomtypes] in ffnonbonded your C and A values each atom has a specific LJ potential shape. Right? So two of them approaching each other in my system will have have the sum of it. Steven On Wed, Jun 12, 2013 at 10:44 AM, Justin Lemkul jalem...@vt.edu wrote: On 6/12/13 5:30 AM, Steven Neumann wrote: Dear Gmx Users, Please, correct me if I am wrong. In ffnonbonded.itp [ atomtypes ] - these are nonbonded parameters between atoms of the same type No, these are the nonbonded parameters that are used when applying combination rules between any atoms. [ nonbond_params ] these are nonbonded parameters between atoms of different type No, these override combination rules. [ pairtypes ] - 1-4 interactions If that is correct why amber force filed has only [atomtypes] column? How nonbonded parameters are calculated between atoms of a different type? The same with charmm - only [atomtypes ] and [pairtypes ] are provided. Would you please explain? Gromos force fields, for instance, have complex ways of generating nonbonded interactions that are not always the same for a given atomtype. Other force fields just use straight combination rules and thus never need [nonbond_params]. -Justin -- ==== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin h**ttp://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 htt**p://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/Searchh**ttp://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 http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==**== Justin A. Lemkul, Ph.D. Research Scientist 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 list
Re: [gmx-users] Nonbonded parameters
grompp is just enumerating the possible combinations of parameters given your inputs. Whether any of those will be used in the simulation will depend on whether atoms of given types are close enough and not excluded. Mark On Wed, Jun 12, 2013 at 12:40 PM, Steven Neumann s.neuman...@gmail.comwrote: I got it. However, I have 60 atoms in my chain all with given C6 and C12 with a combination rule 1. When running grompp: Generated 1830 of the 1830 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 1830 of the 1830 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_X' Analysing residue names: There are: 1Protein residues Analysing Protein... Number of degrees of freedom in T-Coupling group rest is 118.00 This run will generate roughly 2 Mb of data when changing nrexcl in my topology to 0: Generated 1830 of the 1830 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 1830 of the 1830 1-4 parameter combinations Excluding 0 bonded neighbours molecule type 'Protein_chain_X' Analysing residue names: There are: 1Protein residues Analysing Protein... Number of degrees of freedom in T-Coupling group rest is 118.00 This run will generate roughly 2 Mb of data So if I exclude 1-3 interactions I have the same number of nonbonded parameters as well as 1-4 interactions. Can someone explain me this please? On Wed, Jun 12, 2013 at 11:12 AM, Steven Neumann s.neuman...@gmail.com wrote: On Wed, Jun 12, 2013 at 11:05 AM, Justin Lemkul jalem...@vt.edu wrote: On 6/12/13 6:00 AM, Steven Neumann wrote: Thank you. That means that e.g. when two LJ atoms of a different type approaching each other the non bonded LJ potential energy is a sum of two potentials of those atoms? No, please refer to the Gromacs manual for discussion on combination rules and how they fit into the Lennard-Jones equation. -Justin I read it. I used combination rule 1 in which C=4epsSig^6 and A=4epsSig^12 - So that means that when you provide in [atomtypes] in ffnonbonded your C and A values each atom has a specific LJ potential shape. Right? So two of them approaching each other in my system will have have the sum of it. Steven On Wed, Jun 12, 2013 at 10:44 AM, Justin Lemkul jalem...@vt.edu wrote: On 6/12/13 5:30 AM, Steven Neumann wrote: Dear Gmx Users, Please, correct me if I am wrong. In ffnonbonded.itp [ atomtypes ] - these are nonbonded parameters between atoms of the same type No, these are the nonbonded parameters that are used when applying combination rules between any atoms. [ nonbond_params ] these are nonbonded parameters between atoms of different type No, these override combination rules. [ pairtypes ] - 1-4 interactions If that is correct why amber force filed has only [atomtypes] column? How nonbonded parameters are calculated between atoms of a different type? The same with charmm - only [atomtypes ] and [pairtypes ] are provided. Would you please explain? Gromos force fields, for instance, have complex ways of generating nonbonded interactions that are not always the same for a given atomtype. Other force fields just use straight combination rules and thus never need [nonbond_params]. -Justin -- ==== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin http://vt.edu/Pages/Personal/justin h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users http://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Search http://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_Lists http://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080
Re: [gmx-users] Nonbonded parameters
Parameters for possible interactions is not the same as interactions. The latter depend on the configuration and cut-offs... grompp is not doing a neighbor search! Mark On Wed, Jun 12, 2013 at 1:48 PM, Steven Neumann s.neuman...@gmail.comwrote: On Wed, Jun 12, 2013 at 12:45 PM, Mark Abraham mark.j.abra...@gmail.com wrote: grompp is just enumerating the possible combinations of parameters given your inputs. Whether any of those will be used in the simulation will depend on whether atoms of given types are close enough and not excluded. Mark I understand...but why for 60 mer polypeptide there are 1830 nonbonded interactions ? On Wed, Jun 12, 2013 at 12:40 PM, Steven Neumann s.neuman...@gmail.com wrote: I got it. However, I have 60 atoms in my chain all with given C6 and C12 with a combination rule 1. When running grompp: Generated 1830 of the 1830 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 1830 of the 1830 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_X' Analysing residue names: There are: 1Protein residues Analysing Protein... Number of degrees of freedom in T-Coupling group rest is 118.00 This run will generate roughly 2 Mb of data when changing nrexcl in my topology to 0: Generated 1830 of the 1830 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 1830 of the 1830 1-4 parameter combinations Excluding 0 bonded neighbours molecule type 'Protein_chain_X' Analysing residue names: There are: 1Protein residues Analysing Protein... Number of degrees of freedom in T-Coupling group rest is 118.00 This run will generate roughly 2 Mb of data So if I exclude 1-3 interactions I have the same number of nonbonded parameters as well as 1-4 interactions. Can someone explain me this please? On Wed, Jun 12, 2013 at 11:12 AM, Steven Neumann s.neuman...@gmail.com wrote: On Wed, Jun 12, 2013 at 11:05 AM, Justin Lemkul jalem...@vt.edu wrote: On 6/12/13 6:00 AM, Steven Neumann wrote: Thank you. That means that e.g. when two LJ atoms of a different type approaching each other the non bonded LJ potential energy is a sum of two potentials of those atoms? No, please refer to the Gromacs manual for discussion on combination rules and how they fit into the Lennard-Jones equation. -Justin I read it. I used combination rule 1 in which C=4epsSig^6 and A=4epsSig^12 - So that means that when you provide in [atomtypes] in ffnonbonded your C and A values each atom has a specific LJ potential shape. Right? So two of them approaching each other in my system will have have the sum of it. Steven On Wed, Jun 12, 2013 at 10:44 AM, Justin Lemkul jalem...@vt.edu wrote: On 6/12/13 5:30 AM, Steven Neumann wrote: Dear Gmx Users, Please, correct me if I am wrong. In ffnonbonded.itp [ atomtypes ] - these are nonbonded parameters between atoms of the same type No, these are the nonbonded parameters that are used when applying combination rules between any atoms. [ nonbond_params ] these are nonbonded parameters between atoms of different type No, these override combination rules. [ pairtypes ] - 1-4 interactions If that is correct why amber force filed has only [atomtypes] column? How nonbonded parameters are calculated between atoms of a different type? The same with charmm - only [atomtypes ] and [pairtypes ] are provided. Would you please explain? Gromos force fields, for instance, have complex ways of generating nonbonded interactions that are not always the same for a given atomtype. Other force fields just use straight combination rules and thus never need [nonbond_params]. -Justin -- ==== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin http://vt.edu/Pages/Personal/justin h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users http://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at
Re: [gmx-users] Nonbonded parameters
All possible interactions = 60*60/2 = 1800. Where grompp takes another 30 from? On Wed, Jun 12, 2013 at 12:52 PM, Mark Abraham mark.j.abra...@gmail.comwrote: Parameters for possible interactions is not the same as interactions. The latter depend on the configuration and cut-offs... grompp is not doing a neighbor search! Mark On Wed, Jun 12, 2013 at 1:48 PM, Steven Neumann s.neuman...@gmail.com wrote: On Wed, Jun 12, 2013 at 12:45 PM, Mark Abraham mark.j.abra...@gmail.com wrote: grompp is just enumerating the possible combinations of parameters given your inputs. Whether any of those will be used in the simulation will depend on whether atoms of given types are close enough and not excluded. Mark I understand...but why for 60 mer polypeptide there are 1830 nonbonded interactions ? On Wed, Jun 12, 2013 at 12:40 PM, Steven Neumann s.neuman...@gmail.com wrote: I got it. However, I have 60 atoms in my chain all with given C6 and C12 with a combination rule 1. When running grompp: Generated 1830 of the 1830 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 1830 of the 1830 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_X' Analysing residue names: There are: 1Protein residues Analysing Protein... Number of degrees of freedom in T-Coupling group rest is 118.00 This run will generate roughly 2 Mb of data when changing nrexcl in my topology to 0: Generated 1830 of the 1830 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 1830 of the 1830 1-4 parameter combinations Excluding 0 bonded neighbours molecule type 'Protein_chain_X' Analysing residue names: There are: 1Protein residues Analysing Protein... Number of degrees of freedom in T-Coupling group rest is 118.00 This run will generate roughly 2 Mb of data So if I exclude 1-3 interactions I have the same number of nonbonded parameters as well as 1-4 interactions. Can someone explain me this please? On Wed, Jun 12, 2013 at 11:12 AM, Steven Neumann s.neuman...@gmail.com wrote: On Wed, Jun 12, 2013 at 11:05 AM, Justin Lemkul jalem...@vt.edu wrote: On 6/12/13 6:00 AM, Steven Neumann wrote: Thank you. That means that e.g. when two LJ atoms of a different type approaching each other the non bonded LJ potential energy is a sum of two potentials of those atoms? No, please refer to the Gromacs manual for discussion on combination rules and how they fit into the Lennard-Jones equation. -Justin I read it. I used combination rule 1 in which C=4epsSig^6 and A=4epsSig^12 - So that means that when you provide in [atomtypes] in ffnonbonded your C and A values each atom has a specific LJ potential shape. Right? So two of them approaching each other in my system will have have the sum of it. Steven On Wed, Jun 12, 2013 at 10:44 AM, Justin Lemkul jalem...@vt.edu wrote: On 6/12/13 5:30 AM, Steven Neumann wrote: Dear Gmx Users, Please, correct me if I am wrong. In ffnonbonded.itp [ atomtypes ] - these are nonbonded parameters between atoms of the same type No, these are the nonbonded parameters that are used when applying combination rules between any atoms. [ nonbond_params ] these are nonbonded parameters between atoms of different type No, these override combination rules. [ pairtypes ] - 1-4 interactions If that is correct why amber force filed has only [atomtypes] column? How nonbonded parameters are calculated between atoms of a different type? The same with charmm - only [atomtypes ] and [pairtypes ] are provided. Would you please explain? Gromos force fields, for instance, have complex ways of generating nonbonded interactions that are not always the same for a given atomtype. Other force fields just use straight combination rules and thus never need [nonbond_params]. -Justin -- ==== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin http://vt.edu/Pages/Personal/justin h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ====
Re: [gmx-users] Nonbonded parameters
and 1830 1-4 interactions... there are 57 all possible 1-4 interactions On Wed, Jun 12, 2013 at 12:55 PM, Steven Neumann s.neuman...@gmail.comwrote: All possible interactions = 60*60/2 = 1800. Where grompp takes another 30 from? On Wed, Jun 12, 2013 at 12:52 PM, Mark Abraham mark.j.abra...@gmail.comwrote: Parameters for possible interactions is not the same as interactions. The latter depend on the configuration and cut-offs... grompp is not doing a neighbor search! Mark On Wed, Jun 12, 2013 at 1:48 PM, Steven Neumann s.neuman...@gmail.com wrote: On Wed, Jun 12, 2013 at 12:45 PM, Mark Abraham mark.j.abra...@gmail.com wrote: grompp is just enumerating the possible combinations of parameters given your inputs. Whether any of those will be used in the simulation will depend on whether atoms of given types are close enough and not excluded. Mark I understand...but why for 60 mer polypeptide there are 1830 nonbonded interactions ? On Wed, Jun 12, 2013 at 12:40 PM, Steven Neumann s.neuman...@gmail.com wrote: I got it. However, I have 60 atoms in my chain all with given C6 and C12 with a combination rule 1. When running grompp: Generated 1830 of the 1830 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 1830 of the 1830 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_X' Analysing residue names: There are: 1Protein residues Analysing Protein... Number of degrees of freedom in T-Coupling group rest is 118.00 This run will generate roughly 2 Mb of data when changing nrexcl in my topology to 0: Generated 1830 of the 1830 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 1830 of the 1830 1-4 parameter combinations Excluding 0 bonded neighbours molecule type 'Protein_chain_X' Analysing residue names: There are: 1Protein residues Analysing Protein... Number of degrees of freedom in T-Coupling group rest is 118.00 This run will generate roughly 2 Mb of data So if I exclude 1-3 interactions I have the same number of nonbonded parameters as well as 1-4 interactions. Can someone explain me this please? On Wed, Jun 12, 2013 at 11:12 AM, Steven Neumann s.neuman...@gmail.com wrote: On Wed, Jun 12, 2013 at 11:05 AM, Justin Lemkul jalem...@vt.edu wrote: On 6/12/13 6:00 AM, Steven Neumann wrote: Thank you. That means that e.g. when two LJ atoms of a different type approaching each other the non bonded LJ potential energy is a sum of two potentials of those atoms? No, please refer to the Gromacs manual for discussion on combination rules and how they fit into the Lennard-Jones equation. -Justin I read it. I used combination rule 1 in which C=4epsSig^6 and A=4epsSig^12 - So that means that when you provide in [atomtypes] in ffnonbonded your C and A values each atom has a specific LJ potential shape. Right? So two of them approaching each other in my system will have have the sum of it. Steven On Wed, Jun 12, 2013 at 10:44 AM, Justin Lemkul jalem...@vt.edu wrote: On 6/12/13 5:30 AM, Steven Neumann wrote: Dear Gmx Users, Please, correct me if I am wrong. In ffnonbonded.itp [ atomtypes ] - these are nonbonded parameters between atoms of the same type No, these are the nonbonded parameters that are used when applying combination rules between any atoms. [ nonbond_params ] these are nonbonded parameters between atoms of different type No, these override combination rules. [ pairtypes ] - 1-4 interactions If that is correct why amber force filed has only [atomtypes] column? How nonbonded parameters are calculated between atoms of a different type? The same with charmm - only [atomtypes ] and [pairtypes ] are provided. Would you please explain? Gromos force fields, for instance, have complex ways of generating nonbonded interactions that are not always the same for a given atomtype. Other force fields just use straight combination rules and thus never need [nonbond_params]. -Justin -- ==== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin http://vt.edu/Pages/Personal/justin
Re: [gmx-users] Umbrella Sampling Force component output
Thanks Erik On 06/12/2013 01:50 PM, Erik Marklund wrote: Hi, No, I'm afraid not. pull-dim not only determines what components are to be printed, it also determines in what dimensions the force is to be applied during the simulation. Erik On 12 Jun 2013, at 13:32, Kenny Bravo Rodriguez ke...@mpi-muelheim.mpg.de wrote: Dear Gromacs Users, I runned and Umbrella Sampling simulation but I made a mistake in the value of the pull_dim option, so gromacs printed the z component of the force instead of the x component that i need (with the option -pf of mdrun). I have all files from the simulation. Is there a way to get the x component of the force without running the simulation again? Thanks in advanced, Kenny -- 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 -- Kenny Bravo Rodriguez Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 D-45470 Mülheim an der Ruhr Germany Phone: +49 (0)208 306 2160 Email:ke...@mpi-muelheim.mpg.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] Nonbonded parameters
How many atom *types* are there? On Wed, Jun 12, 2013 at 1:57 PM, Steven Neumann s.neuman...@gmail.comwrote: and 1830 1-4 interactions... there are 57 all possible 1-4 interactions On Wed, Jun 12, 2013 at 12:55 PM, Steven Neumann s.neuman...@gmail.com wrote: All possible interactions = 60*60/2 = 1800. Where grompp takes another 30 from? On Wed, Jun 12, 2013 at 12:52 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Parameters for possible interactions is not the same as interactions. The latter depend on the configuration and cut-offs... grompp is not doing a neighbor search! Mark On Wed, Jun 12, 2013 at 1:48 PM, Steven Neumann s.neuman...@gmail.com wrote: On Wed, Jun 12, 2013 at 12:45 PM, Mark Abraham mark.j.abra...@gmail.com wrote: grompp is just enumerating the possible combinations of parameters given your inputs. Whether any of those will be used in the simulation will depend on whether atoms of given types are close enough and not excluded. Mark I understand...but why for 60 mer polypeptide there are 1830 nonbonded interactions ? On Wed, Jun 12, 2013 at 12:40 PM, Steven Neumann s.neuman...@gmail.com wrote: I got it. However, I have 60 atoms in my chain all with given C6 and C12 with a combination rule 1. When running grompp: Generated 1830 of the 1830 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 1830 of the 1830 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_X' Analysing residue names: There are: 1Protein residues Analysing Protein... Number of degrees of freedom in T-Coupling group rest is 118.00 This run will generate roughly 2 Mb of data when changing nrexcl in my topology to 0: Generated 1830 of the 1830 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 1830 of the 1830 1-4 parameter combinations Excluding 0 bonded neighbours molecule type 'Protein_chain_X' Analysing residue names: There are: 1Protein residues Analysing Protein... Number of degrees of freedom in T-Coupling group rest is 118.00 This run will generate roughly 2 Mb of data So if I exclude 1-3 interactions I have the same number of nonbonded parameters as well as 1-4 interactions. Can someone explain me this please? On Wed, Jun 12, 2013 at 11:12 AM, Steven Neumann s.neuman...@gmail.com wrote: On Wed, Jun 12, 2013 at 11:05 AM, Justin Lemkul jalem...@vt.edu wrote: On 6/12/13 6:00 AM, Steven Neumann wrote: Thank you. That means that e.g. when two LJ atoms of a different type approaching each other the non bonded LJ potential energy is a sum of two potentials of those atoms? No, please refer to the Gromacs manual for discussion on combination rules and how they fit into the Lennard-Jones equation. -Justin I read it. I used combination rule 1 in which C=4epsSig^6 and A=4epsSig^12 - So that means that when you provide in [atomtypes] in ffnonbonded your C and A values each atom has a specific LJ potential shape. Right? So two of them approaching each other in my system will have have the sum of it. Steven On Wed, Jun 12, 2013 at 10:44 AM, Justin Lemkul jalem...@vt.edu wrote: On 6/12/13 5:30 AM, Steven Neumann wrote: Dear Gmx Users, Please, correct me if I am wrong. In ffnonbonded.itp [ atomtypes ] - these are nonbonded parameters between atoms of the same type No, these are the nonbonded parameters that are used when applying combination rules between any atoms. [ nonbond_params ] these are nonbonded parameters between atoms of different type No, these override combination rules. [ pairtypes ] - 1-4 interactions If that is correct why amber force filed has only [atomtypes] column? How nonbonded parameters are calculated between atoms of a different type? The same with charmm - only [atomtypes ] and [pairtypes ] are provided. Would you please explain? Gromos force fields, for instance, have complex ways of generating nonbonded interactions that are not always the same for a given atomtype. Other force fields just use straight combination rules and thus never need [nonbond_params]. -Justin -- ====
Re: [gmx-users] Nonbonded parameters
60 types of atoms and 60 atoms in total belonging to one residue On Wed, Jun 12, 2013 at 12:59 PM, Mark Abraham mark.j.abra...@gmail.comwrote: How many atom *types* are there? On Wed, Jun 12, 2013 at 1:57 PM, Steven Neumann s.neuman...@gmail.com wrote: and 1830 1-4 interactions... there are 57 all possible 1-4 interactions On Wed, Jun 12, 2013 at 12:55 PM, Steven Neumann s.neuman...@gmail.com wrote: All possible interactions = 60*60/2 = 1800. Where grompp takes another 30 from? On Wed, Jun 12, 2013 at 12:52 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Parameters for possible interactions is not the same as interactions. The latter depend on the configuration and cut-offs... grompp is not doing a neighbor search! Mark On Wed, Jun 12, 2013 at 1:48 PM, Steven Neumann s.neuman...@gmail.com wrote: On Wed, Jun 12, 2013 at 12:45 PM, Mark Abraham mark.j.abra...@gmail.com wrote: grompp is just enumerating the possible combinations of parameters given your inputs. Whether any of those will be used in the simulation will depend on whether atoms of given types are close enough and not excluded. Mark I understand...but why for 60 mer polypeptide there are 1830 nonbonded interactions ? On Wed, Jun 12, 2013 at 12:40 PM, Steven Neumann s.neuman...@gmail.com wrote: I got it. However, I have 60 atoms in my chain all with given C6 and C12 with a combination rule 1. When running grompp: Generated 1830 of the 1830 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 1830 of the 1830 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_X' Analysing residue names: There are: 1Protein residues Analysing Protein... Number of degrees of freedom in T-Coupling group rest is 118.00 This run will generate roughly 2 Mb of data when changing nrexcl in my topology to 0: Generated 1830 of the 1830 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 1830 of the 1830 1-4 parameter combinations Excluding 0 bonded neighbours molecule type 'Protein_chain_X' Analysing residue names: There are: 1Protein residues Analysing Protein... Number of degrees of freedom in T-Coupling group rest is 118.00 This run will generate roughly 2 Mb of data So if I exclude 1-3 interactions I have the same number of nonbonded parameters as well as 1-4 interactions. Can someone explain me this please? On Wed, Jun 12, 2013 at 11:12 AM, Steven Neumann s.neuman...@gmail.com wrote: On Wed, Jun 12, 2013 at 11:05 AM, Justin Lemkul jalem...@vt.edu wrote: On 6/12/13 6:00 AM, Steven Neumann wrote: Thank you. That means that e.g. when two LJ atoms of a different type approaching each other the non bonded LJ potential energy is a sum of two potentials of those atoms? No, please refer to the Gromacs manual for discussion on combination rules and how they fit into the Lennard-Jones equation. -Justin I read it. I used combination rule 1 in which C=4epsSig^6 and A=4epsSig^12 - So that means that when you provide in [atomtypes] in ffnonbonded your C and A values each atom has a specific LJ potential shape. Right? So two of them approaching each other in my system will have have the sum of it. Steven On Wed, Jun 12, 2013 at 10:44 AM, Justin Lemkul jalem...@vt.edu wrote: On 6/12/13 5:30 AM, Steven Neumann wrote: Dear Gmx Users, Please, correct me if I am wrong. In ffnonbonded.itp [ atomtypes ] - these are nonbonded parameters between atoms of the same type No, these are the nonbonded parameters that are used when applying combination rules between any atoms. [ nonbond_params ] these are nonbonded parameters between atoms of different type No, these override combination rules. [ pairtypes ] - 1-4 interactions If that is correct why amber force filed has only [atomtypes] column? How nonbonded parameters are calculated between atoms of a different type? The same with charmm - only [atomtypes ] and [pairtypes ] are provided. Would you please explain? Gromos force
Re: [gmx-users] Nonbonded parameters
On 6/12/13 8:01 AM, Steven Neumann wrote: 60 types of atoms and 60 atoms in total belonging to one residue The number of possible combinations is (N(N+1))/2, thus you get 1830 from 60 atom types. -Justin On Wed, Jun 12, 2013 at 12:59 PM, Mark Abraham mark.j.abra...@gmail.comwrote: How many atom *types* are there? On Wed, Jun 12, 2013 at 1:57 PM, Steven Neumann s.neuman...@gmail.com wrote: and 1830 1-4 interactions... there are 57 all possible 1-4 interactions On Wed, Jun 12, 2013 at 12:55 PM, Steven Neumann s.neuman...@gmail.com wrote: All possible interactions = 60*60/2 = 1800. Where grompp takes another 30 from? On Wed, Jun 12, 2013 at 12:52 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Parameters for possible interactions is not the same as interactions. The latter depend on the configuration and cut-offs... grompp is not doing a neighbor search! Mark On Wed, Jun 12, 2013 at 1:48 PM, Steven Neumann s.neuman...@gmail.com wrote: On Wed, Jun 12, 2013 at 12:45 PM, Mark Abraham mark.j.abra...@gmail.com wrote: grompp is just enumerating the possible combinations of parameters given your inputs. Whether any of those will be used in the simulation will depend on whether atoms of given types are close enough and not excluded. Mark I understand...but why for 60 mer polypeptide there are 1830 nonbonded interactions ? On Wed, Jun 12, 2013 at 12:40 PM, Steven Neumann s.neuman...@gmail.com wrote: I got it. However, I have 60 atoms in my chain all with given C6 and C12 with a combination rule 1. When running grompp: Generated 1830 of the 1830 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 1830 of the 1830 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_X' Analysing residue names: There are: 1Protein residues Analysing Protein... Number of degrees of freedom in T-Coupling group rest is 118.00 This run will generate roughly 2 Mb of data when changing nrexcl in my topology to 0: Generated 1830 of the 1830 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 1830 of the 1830 1-4 parameter combinations Excluding 0 bonded neighbours molecule type 'Protein_chain_X' Analysing residue names: There are: 1Protein residues Analysing Protein... Number of degrees of freedom in T-Coupling group rest is 118.00 This run will generate roughly 2 Mb of data So if I exclude 1-3 interactions I have the same number of nonbonded parameters as well as 1-4 interactions. Can someone explain me this please? On Wed, Jun 12, 2013 at 11:12 AM, Steven Neumann s.neuman...@gmail.com wrote: On Wed, Jun 12, 2013 at 11:05 AM, Justin Lemkul jalem...@vt.edu wrote: On 6/12/13 6:00 AM, Steven Neumann wrote: Thank you. That means that e.g. when two LJ atoms of a different type approaching each other the non bonded LJ potential energy is a sum of two potentials of those atoms? No, please refer to the Gromacs manual for discussion on combination rules and how they fit into the Lennard-Jones equation. -Justin I read it. I used combination rule 1 in which C=4epsSig^6 and A=4epsSig^12 - So that means that when you provide in [atomtypes] in ffnonbonded your C and A values each atom has a specific LJ potential shape. Right? So two of them approaching each other in my system will have have the sum of it. Steven On Wed, Jun 12, 2013 at 10:44 AM, Justin Lemkul jalem...@vt.edu wrote: On 6/12/13 5:30 AM, Steven Neumann wrote: Dear Gmx Users, Please, correct me if I am wrong. In ffnonbonded.itp [ atomtypes ] - these are nonbonded parameters between atoms of the same type No, these are the nonbonded parameters that are used when applying combination rules between any atoms. [ nonbond_params ] these are nonbonded parameters between atoms of different type No, these override combination rules. [ pairtypes ] - 1-4 interactions If that is correct why amber force filed has only [atomtypes] column? How nonbonded parameters are calculated between atoms of a different type? The same with charmm - only [atomtypes ] and [pairtypes ] are provided. Would you please explain? Gromos force fields, for instance, have complex ways of generating nonbonded interactions that are not always the same for a given atomtype. Other force fields just use straight combination rules and thus never need [nonbond_params]. -Justin -- ==== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem. vt.edu/Pages/Personal/justin http://vt.edu/Pages/Personal/justin h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
Re: [gmx-users] Nonbonded parameters
So how come 1830 1-4 interaction? There should be 57 of 1-4 interactions -- 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] Nonbonded parameters
On 6/12/13 8:16 AM, Steven Neumann wrote: So how come 1830 1-4 interaction? There should be 57 of 1-4 interactions Mark already told you this - interactions that exist are different from possible interactions. You may have 57 interactions, but that's specific to your system because of how many atoms there are (which is also independent of how many atom types are used therein). grompp generates a bunch of information (a matrix of possible interactions that could theoretically occur with N atom types); whether or not it uses that information is not necessarily relevant. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] Re: gromacs 4.6.2 MPI distribution location problems
On Wed, Jun 12, 2013 at 12:42 AM, sirishkaushik kaushik.lakkar...@gmail.com wrote: Note that this works fine with 4.5.5. when I installed using: ./configure CPPFLAGS=-I/home/kaushik/fftw-new/include LDFLAGS=-L/home/kaushik/fftw-new/lib --enable-mpi --prefix /home/kaushik/gromacs_executable/gromacs-old ldd mdrun on the 4.5.5 version correctly points to the fftw and the mpi locations: linux-vdso.so.1 = (0x7fff6a302000) libfftw3f.so.3 = /home/kaushik/fftw-new/lib/libfftw3f.so.3 (0x7f2e7a6e2000) libmpi.so.1 = /usr/local/lib/libmpi.so.1 (0x7f2e7a34) libnsl.so.1 = /lib/libnsl.so.1 (0x7f2e7a11b000) libm.so.6 = /lib/libm.so.6 (0x7f2e79e99000) libdl.so.2 = /lib/libdl.so.2 (0x7f2e79c95000) libnuma.so.1 = /usr/lib/libnuma.so.1 (0x7f2e79a8c000) librt.so.1 = /lib/librt.so.1 (0x7f2e79884000) libutil.so.1 = /lib/libutil.so.1 (0x7f2e79681000) libpthread.so.0 = /lib/libpthread.so.0 (0x7f2e79464000) libc.so.6 = /lib/libc.so.6 (0x7f2e79102000) libmpi.so.0 = /usr/lib/libmpi.so.0 (0x7f2e78e52000) /lib64/ld-linux-x86-64.so.2 (0x7f2e7a9f4000) libopen-rte.so.0 = /usr/lib/libopen-rte.so.0 (0x7f2e78c05000) libopen-pal.so.0 = /usr/lib/libopen-pal.so.0 (0x7f2e789b) However, with 4.6.2, when I install using: cmake -DCMAKE_INSTALL_PREFIX=/home/kaushik/gromacs_executable/gromacs-mpi -DGMX_THREADS=DGMX_X11=OFF -DGMX_MPI=ON -DCMAKE_PREFIX_PATH=/home/kaushik/fftw-new -DGMX_DEFAULT_SUFFIX=OFF -DMPI_INCLUDE_PATH=/usr/local/include -DMPI_COMPILER=/usr/local/bin/mpicxx cmake -DCMAKE_C_COMPILER=/usr/local/bin/mpicc should Just Work. its now pointing to the wrong MPI libraries causing the crash with the mpirun: ldd mdrun: linux-vdso.so.1 = (0x7fffba9ff000) libfftw3f.so.3 = /home/kaushik/fftw-new/lib/libfftw3f.so.3 (0x7f32c6785000) libmpi_cxx.so.0 = /usr/lib/libmpi_cxx.so.0 (0x7f32c655e000) libmpi.so.0 = /usr/lib/libmpi.so.0 (0x7f32c62ae000) libdl.so.2 = /lib/libdl.so.2 (0x7f32c60aa000) libm.so.6 = /lib/libm.so.6 (0x7f32c5e27000) libnuma.so.1 = /usr/lib/libnuma.so.1 (0x7f32c5c1f000) librt.so.1 = /lib/librt.so.1 (0x7f32c5a17000) libnsl.so.1 = /lib/libnsl.so.1 (0x7f32c57fe000) libutil.so.1 = /lib/libutil.so.1 (0x7f32c55fb000) libpthread.so.0 = /lib/libpthread.so.0 (0x7f32c53df000) libgomp.so.1 = /usr/local/lib64/libgomp.so.1 (0x7f32c51d) libc.so.6 = /lib/libc.so.6 (0x7f32c4e6e000) libstdc++.so.6 = /usr/local/lib64/libstdc++.so.6 (0x7f32c4b67000) libgcc_s.so.1 = /usr/local/lib64/libgcc_s.so.1 (0x7f32c4951000) libopen-rte.so.0 = /usr/lib/libopen-rte.so.0 (0x7f32c4705000) /lib64/ld-linux-x86-64.so.2 (0x7f32c6a97000) libopen-pal.so.0 = /usr/lib/libopen-pal.so.0 (0x7f32c44af000) Is this a potential bug, as in the gromacs compilation is picking up the /usr/lib/ and /usr/include (old MPI locations) despite manually specifying it using -DMPI_INCLUDE, etc? Perhaps, but it is not yet clear where the problem lies. In cmake, we try to compile an MPI test program with the compiler you've made available, and just use that compiler if it works. This combines nicely with modern MPI wrapper compilers, hence the above suggestion. Otherwise, in cmake we try to do some detection, and that presumably leads to your symptoms. It might be possible to work around that by setting CMAKE_PREFIX_PATH=/usr/local, so that the detection finds the version you want. 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
[gmx-users] charmm27 in gromacs- grompp error
Dear all, I am using charmm27 forcefield in gromacs for performing all atom simulations (system comprising of DOPC, cholesteryl ester and protein) .I got the itp file for dopc from the lipid book in which they have mentioned #include charmm27.ff/ffbonded.itp and charmm27.ff/ffnonbonded.itp to source to these for the parameters of each bond, angle dihedral etc based on the atom types instead of mentioning explicitly each numerical value from the gromacs directory.But it could not read the file and displayed: Syntax error - File ffbonded.itp, line 2 Last line read: '[ atomtypes ]' Invalid order for directive defaults When I commented those lines and again ran grompp, it generated the following error: No default Angle types No default Ryckaert-Bell. types. Kindly suggest me in this issue. Earnestly awaiting a reply, Revathi M.S. Research Scholar Indian Institute Of Technology, Madras India -- 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 in gromacs- grompp error
Sounds like either you're following wrong instructions, or not following them correctly. Please double check and/or take up the issue with the author. Mark On Wed, Jun 12, 2013 at 3:03 PM, Revthi Sanker revthi.san...@yahoo.comwrote: Dear all, I am using charmm27 forcefield in gromacs for performing all atom simulations (system comprising of DOPC, cholesteryl ester and protein) .I got the itp file for dopc from the lipid book in which they have mentioned #include charmm27.ff/ffbonded.itp and charmm27.ff/ffnonbonded.itp to source to these for the parameters of each bond, angle dihedral etc based on the atom types instead of mentioning explicitly each numerical value from the gromacs directory.But it could not read the file and displayed: Syntax error - File ffbonded.itp, line 2 Last line read: '[ atomtypes ]' Invalid order for directive defaults When I commented those lines and again ran grompp, it generated the following error: No default Angle types No default Ryckaert-Bell. types. Kindly suggest me in this issue. Earnestly awaiting a reply, Revathi M.S. Research Scholar Indian Institute Of Technology, Madras India -- 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 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] Details of umbrella sampling simulation
Dear users, What is the algorithm of umbrella sampling simulation ? And can anyone who had experience in this explain pulling force to me ? Thankul and regards, ~Thu -- 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] Quartic Angle
Dear Gmx Users, I run a simulation with quartic angle potential. These function has two minima at 100 at 120 degrees. However, seems from my simulation that it is not applied... all angles are around 180 degrees and my chain is a line chain (straight). I have in my topology [ angles ] ; i j k funct th0 C0 C1 C2 C3 C4 123601389.5-46.90530.59033 -0.00328291 0.0680894 in the log file the quartic potential is shown every time. Can it be the reason of th0 to be zero? Steven -- 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] Re: Free Energy Calculations in Gromacs
Thanks Justin and Professor Shirts. The gmxdump on the resulting tpr did indeed solve a lot of my problems. Thanks again. -- View this message in context: http://gromacs.5086.x6.nabble.com/Free-Energy-Calculations-in-Gromacs-tp5007495p5009115.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Re: Details of umbrella sampling simulation
Hi, Please see the following links: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/ http://wires.wiley.com/WileyCDA/WiresArticle/wisId-WCMS66.html I think you will understand the concept of the pulling force once you go through either of the links. It's basically the force to restraint a particular collective variable around a certain value for sampling around that region in phase space. -- View this message in context: http://gromacs.5086.x6.nabble.com/Details-of-umbrella-sampling-simulation-tp5009113p5009116.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] stay at some temperature during annealing
Hi Guys, sorry I replay so late, the annealing_npoints should be 4 4 4, which I incorrectly defined to 3 3 3. the problem solved. Thanks! Justin On Tue, Jun 11, 2013 at 6:36 AM, Dr. Vitaly Chaban vvcha...@gmail.comwrote: On Tue, Jun 11, 2013 at 12:52 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/11/13 1:11 AM, mu xiaojia wrote: Hi guys, I am using simulated annealing for my protein+water+Ion system, I tried to let the system stay at some temperature for a while, e.g.: stay at 600k from 3000ps to 1 ps, then gradually cool it down to 298k, so my mdp is like: annealing_time = 0 3000 1 2 0 3000 1 2 0 3000 1 2 annealing_temp = 298 600 600 298 298 600 600 298 298 600 600 298 however, error message is: Found 12 annealing_time values, wanter 9 apparently, the 600 600 does not work, does anyone have any suggestion, or I could only separate the simulation? Thanks very much! There is a problem with the number of temperature coupling groups. You have defined less than you expect, as the program requests only 9 values. So, refer to the number of points to T annealing, which you do not list here. Dr. Vitaly Chaban -- 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 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: Enthalpy Confusion
On 2013-06-11 23:31, Jeffery Perkins wrote: or should i be doing U+V*ref_p = H? More specifically, U + V*ref_p = H H isn't really meaningful thing. I mean, you can define something such that H* = H, but that's not really thermodynamics. sorry I always have issues deciding how to talk about this stuff, so thanks for putting up with my terrible notation =) example system gives H = -1168 kJ/mol and i find H = -725 kJ/mol either Interesting. What material at what phase conditions? For liquids, the PV contribution should be very small. I hadn't really thought about that... but the system is a monatomic Lennard-Jones particle (uncharged sigma = 0.35 nm epsilon = 2 kJ/mol mass = 40 amu) which should be a liquid at the conditions I was looking at, P=1000 bar, T = 300 K using phase diagram in: Equation of state for the Lennard-Jones fluid, J. J. Nicolas et al., MOLECULAR PHYSICS, 1979, VOL. 37, No. 5, 1429-1454 the U is -1600 and the pV is 880 when manually done, around 400 from g_energy Here's the code: /* This is pV (in kJ/mol). The pressure is the reference pressure, not the instantaneous pressure */ pv = vol*md-ref_p/PRESFAC; add_ebin(md-ebin, md-ipv, 1, pv, bSum); enthalpy = pv + enerd-term[F_ETOT]; What is your volume? What is Etot? PRESFAC ~ 16.6 -- View this message in context: http://gromacs.5086.x6.nabble.com/Enthalpy-Confusion-tp5009053p5009068.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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 -- 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] Quartic Angle
On 6/12/13 10:01 AM, Steven Neumann wrote: Dear Gmx Users, I run a simulation with quartic angle potential. These function has two minima at 100 at 120 degrees. However, seems from my simulation that it is not applied... all angles are around 180 degrees and my chain is a line chain (straight). I have in my topology [ angles ] ; i j k funct th0 C0 C1 C2 C3 C4 123601389.5-46.90530.59033 -0.00328291 0.0680894 in the log file the quartic potential is shown every time. Can it be the reason of th0 to be zero? That's what I'd suspect. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] Re: Details of umbrella sampling simulation
Thank JW so much :-) On Wed, Jun 12, 2013 at 10:30 PM, JW Gibbs hanniballecte...@gmail.comwrote: Hi, Please see the following links: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/ http://wires.wiley.com/WileyCDA/WiresArticle/wisId-WCMS66.html I think you will understand the concept of the pulling force once you go through either of the links. It's basically the force to restraint a particular collective variable around a certain value for sampling around that region in phase space. -- View this message in context: http://gromacs.5086.x6.nabble.com/Details-of-umbrella-sampling-simulation-tp5009113p5009116.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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 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] Fw: charmm27 in gromacs- grompp error
Dear all, I am using charmm27 forcefield in gromacs for performing all atom simulations (system comprising of DOPC, cholesteryl ester and protein) .I got the itp file for dopc from the lipid book in which they have mentioned #include charmm27.ff/ffbonded.itp and charmm27.ff/ffnonbonded.itp to source to these for the parameters of each bond, angle dihedral etc based on the atom types instead of mentioning explicitly each numerical value from the gromacs directory.But it could not read the file and displayed: Syntax error - File ffbonded.itp, line 2 Last line read: '[ atomtypes ]' Invalid order for directive defaults When I commented those lines and again ran grompp, it generated the following error: No default Angle types No default Ryckaert-Bell. types. Kindly suggest me in this issue. Earnestly awaiting a reply, Revathi M.S. Research Scholar Indian Institute Of Technology, Madras India -- 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
