[gmx-users] A problem with potential energy values and openMP
Dear Gromacs users, I have been working with Gromacs v. 5.0.4 by using its MPI/OPENMP – parallelization. While studying outputs of mdrun with input argument ”ntomp” (shell command ”gmx_mpi mdrun -ntomp i” where i = 1,2 or 4), the potential energy values seemed to differ. My typical demo run included 100 steps and the potential energy values were checked for the first (initial) step. Below, the obtained potential energy values are presented for two different energy groups and for three different ”ntomp” values (unit for potential energy: kJ/mol) SystemProt – Sol ntomp: 1-193754.7-193733.2 ntomp: 2 -193741.3-193795.4 ntomp: 4 (”default” run)-193744.7-193758.7 A more detailed investigation showed that the deviations can be seen in the values of short – range Coulomb forces (other Coulomb short - range values than the values of ”SOL-SOL” system in the ”Prot-Sol” simulations differed less than 1 kJ/mol. The values in "SOL-SOL" system mostly induced the differences). I use ”PME” as ”coulombtype” here, but the potential energy values also differed when using ”cut-off” and again, the differences were noticed especially in the case of the short – range Coulomb forces. The question is: can one expect such differences in potential energy values when using openMP parallelization or is this a simple user error? Gromacs was run in a server for which detailed information is printed below by using command ”lscpu”: " Architecture: x86_64 CPU op-mode(s):32-bit, 64-bit Byte Order:Little Endian CPU(s):4 On-line CPU(s) list: 0-3 Thread(s) per core:1 Core(s) per socket:4 Socket(s): 1 NUMA node(s): 1 Vendor ID: GenuineIntel CPU family:6 Model: 44 Stepping: 2 CPU MHz: 2400.000 BogoMIPS: 4799.98 Virtualization:VT-x L1d cache: 32K L1i cache: 32K L2 cache: 256K L3 cache: 12288K NUMA node0 CPU(s): 0-3 " For example, the ”default” run (with shell command ”gmx_mpi mdrun”) produces the following info: ” Using 1 MPI process Using 4 OpenMP threads No GPUs detected on host xxx.xxx.jyu.fi ” Thank you. M-J Vesterinen University of Jyväskylä -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] PBC
Hi Mark Thank you. I suppose grid can be used without PBC specially when the system is in vacuum. There are some parameters in the .mdp file that I haven't defined and I don't want them to be applied during simulation. However in the mdout.mdp They are present eg. gen-seed, emtol, ewald-rtol, Do they play a role in the simulation? Thanks! On Mon, Oct 5, 2015 at 2:26 PM, mah maz wrote: > Hi Mark, > Thanks. It seems the default is pbc =xyz. But my question is if I don't > use PBC, can I use grid, or grid is only meaningful when PBC is defined? > > On Mon, Oct 5, 2015 at 11:07 AM, mah maz wrote: > >> Dear users, >> >> If I dont define pbc=no, what is the default type for gromacs? Is it >> right if I dont use pbc=no in my system while using grid for ns-type? >> >> thank you. >> > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] pdb2gmx error
Thanks for the reply Justin. I unfortunately cannot currently disclose the files that I'm working on. Based on the info presented, would you say that it's an issue with the force field definition or with the actual protein topology? I am not planning on using amber03 in my simulations at the moment, so this specific warning is not that important, but I can't help but wonder if this warning means something is off in the topology. On 7 October 2015 at 23:05, Justin Lemkul wrote: > > > On 10/7/15 5:03 PM, Dries Van Rompaey wrote: > >> Thanks Justin, that makes sense! I'm wondering why none of the other >> proline residues triggered that warning though? The same procedure works >> like a charm with other proteins. >> > > Without access to all of the files you're looking at, the best I can do is > shrug my shoulders because that doesn't make any sense. Some prolines work > and one doesn't? That's just not logical. > > -Justin > > > On 7 Oct 2015 10:59 pm, "Justin Lemkul" wrote: >> >> >>> >>> On 10/7/15 3:01 PM, Dries Van Rompaey wrote: >>> >>> Hi Mark, This is Gromacs 5.0.4. This is a non-terminal residue. The command line used is: gmx pdb2gmx -f complex.pdb -o complex.gro (-ignh) I tried this procedure with and without ignh flag. As far as I know, specbonds is not in play. Non-terminal proline does not have an amide H. If your force field .rtp >>> file claims to use such an atom used in a dihedral (which is what the >>> error >>> message tells you is happening), find out who altered the file and >>> reprimand them :) >>> >>> -Justin >>> >>> Kind regards, >>> Dries On 7 October 2015 at 20:56, Mark Abraham wrote: Hi, > > Is it terminal? Are there specbonds in play? What's the GROMACS > version? > What's your pdb2gmx command line? :-) > > Mark > > On Wed, Oct 7, 2015 at 8:43 PM Dries Van Rompaey < > dries.vanromp...@gmail.com> > wrote: > > Hi everyone, > >> >> I'm getting the following warning when I try to run pdb2gmx on my >> protein >> structure: >> >> WARNING: WARNING: Residue 168 named PRO of a molecule in the input >> file >> >> was > > mapped to an entry in the topology database, but the atom H used in an >> interaction of type dihedral in that entry is not found in the input >> >> file. > > Perhaps your atom and/or residue naming needs to be fixed. >> >> This warning is only present when I use the AMBER03 forcefield, all >> other >> forcefields seem to work fine. I have tried this with both a structure >> without hydrogens as well as a structure with hydrogens added, both >> with >> and without the -ignh flag. I tried looking at the amber03 database >> files >> as well as the amber99sb-ildn database files (amber99sb-ildn works >> just >> fine), but I could not find any reason why this particular residue >> would >> >> be > > problematic. pdb2gmx does not find any problems with the other proline >> residues in the protein (which look identical), so I am puzzled as to >> what's causing this. >> >> The proline residue is: >> ATOM 1384 N PRO A 168 274.650 45.241 24.167 1.00180.63 >> N >> ATOM 1385 CA PRO A 168 273.508 44.823 23.370 1.00180.63 >> C >> ATOM 1386 CD PRO A 168 275.844 45.381 23.346 1.00180.63 >> C >> ATOM 1387 CB PRO A 168 274.071 44.405 22.014 1.00180.63 >> C >> ATOM 1388 CG PRO A 168 275.381 45.194 21.892 1.00180.63 >> C >> ATOM 1389 C PRO A 168 272.551 43.776 23.888 1.00180.63 >> C >> ATOM 1390 O PRO A 168 271.478 43.646 23.304 1.00180.63 >> O >> >> Does anyone know what's going on here? >> >> Thanks in advance! >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> >> -- >> > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > > > -- >>> == >>> >>> Justin A. Lemkul, Ph.D. >>> Ruth L. Kirschstein NRSA Postdoctoral Fellow >>> >>> D
[gmx-users] Dftb as qmmm method with gromacs
Hello all, I want to use dftb as a qmmm method with gromacs as explained in a recent research article " http://onlinelibrary.wiley.com/doi/10.1002/jcc.24029/abstract";. When I am trying to compile gromacs-5.0 with dftb using flag " *-DGMX_QMMM_DFTB*", the cmake .. command is terminating with the following error: Parse error in command line argument: -DGMX_QMMM_DFTB Should be: VAR:type=value CMake Error: No cmake script provided. CMake Error: Problem processing arguments. Aborting. I have followed all the instructions provided in the manual at website " http://cbp.cfn.kit.edu/joomla/index.php/downloads/18-gromacs-with-qm-mm-using-dftb3";. Please help..!!! With regards, Padmani -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Fwd: Gromacs
Respected Sir, Though im finshed upto production step of protein metal complexes, topology file couldnt be created and there is no information about any atoms in my pdb file. the created topology file are shown below ; ;File 'ebolaag.top' was generated ;By user: onbekend (0) ;On host: onbekend ;At date: Wed Oct 7 16:06:22 2015 ; ;This is a standalone topology file ; ;It was generated using program: ;pdb2gmx_d - VERSION 4.5 ; ;Command line was: ;./pdb2gmx_d -f ebolaag.pdb -o ebolaag.gro -p ebolaag.top -ignh ; ;Force field was read from the standard Gromacs share directory. ; ; Include forcefield parameters #include "oplsaa.ff/forcefield.itp" ; Include chain topologies #include "ebolaag_Protein_chain_A.itp" #include "ebolaag_Ion_chain_A2.itp" ; Include water topology #include "oplsaa.ff/tip4p.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include "oplsaa.ff/ions.itp" [ system ] ; Name Protein in water [ molecules ] ; Compound#mols Protein_chain_A 1 Ion_chain_A21 SOL 4673 I can't understand what is the problem, so pls tell me what could be the reason for this. Sincierly, *Saranya Vasudevan,* *Research Scholar,* *Molecular Quantum Mechanics Laboratory,* *Department of Physics,* *Bharathiar University,* *Coimbatore-46* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Free Energy of Liquid Water
If ALL the particles are changing with the free energy coupling parameter, then GROMACS will slow down quite a bit. If only one molecule is changing, then it shouldn't be that much slower (20-30% slower?) But without .mdp and.top files, it's hard to say exactly what is happening. On Wed, Oct 7, 2015 at 11:08 PM, Nathan K Houtz wrote: > Thanks for explaining, (and Professor Farais de Moura as well) that makes > sense. > > On a different note, I've noticed a huge difference in performance between my > equillibration run and my actual simulation, and I'm wondering if this is > normal. For comparison, I ran a couple small (meaningless) simulations where > the only difference was the collection of free energy information and Gromacs > slows down by a factor of 39. I had been under the impression that I would be > able to do each simulation in just under an hour but now it looks like it > will take the better part of two days, which is too much. I'll just have to > run shorter or fewer simulations if I can't improve that, but I'm hoping I'm > just doing something wrong. I'm essentially using modified versions of the > .mdp file I found for this tutorial: > http://www.alchemistry.org/wiki/GROMACS_4.6_example:_Direct_ethanol_solvation_free_energy. > I changed things like turning off the pressure coupling, changing the > temperature, etc. The settings for free energy calculations are unchanged. Is > the calculation of dh/dl re > ally that expensive, or is this abnormal? > > Thank you for the help as always. Regards, > Nathan H. > > - Original Message - > From: "Michael Shirts" > To: "Discussion list for GROMACS users" > Cc: "gromacs org gmx-users" > Sent: Tuesday, October 6, 2015 3:05:38 PM > Subject: Re: [gmx-users] Free Energy of Liquid Water > > For a pure fluid, G = N \mu. And \mu = (dG/dN)_(T,P). So you only > need to change one molecule to ideal gas to get the change in free > energy. The free energy of transfer of water from liquid to gas is > indeed the free energy of solvation of one water molecule in bath of > water. So there's a reason why you're just finding tutorials of > solvation free energies! > > On Thu, Oct 1, 2015 at 10:44 PM, Nathan K Houtz wrote: >> Hi everyone, >> >> I would like to use Gromacs to do Thermodynamic Integration (TI) from liquid >> water (TIP4P model) to an ideal gas, to find the relative free energy. To do >> this, I believe one generally integrates above the critical point by >> increasing the temperature above the critical temperature and then relaxing >> the pressure until the system is a diffuse gas. The mdp options >> documentation is helpful, and I went through an ethanol solvation tutorial, >> but there doesn't appear to be a "pressure-lambda" or a "volume-lambda" >> option that I could use to do the second part. How can I get Gromacs to >> calculate the dh/dl derivative while relaxing the pressure? >> >> In addition, all of the tutorials I found for thermodynamic integration were >> for finding solvation free energies. The coulomb and VDW forces are >> essentially changed from "completely on" to "completely off". But in my >> case, I'd like to change the temperature and pressure between two nonzero >> values. I don't want to begin my simulation at 0K and 0atm, but lambda >> *must* go from 0 to 1. How can I define both starting and ending points for >> the temperature and pressure (or volume, or density)? >> >> Thanks for your help! >> Nathan H. >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a >> mail to gmx-users-requ...@gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Free Energy of Liquid Water
Thanks for explaining, (and Professor Farais de Moura as well) that makes sense. On a different note, I've noticed a huge difference in performance between my equillibration run and my actual simulation, and I'm wondering if this is normal. For comparison, I ran a couple small (meaningless) simulations where the only difference was the collection of free energy information and Gromacs slows down by a factor of 39. I had been under the impression that I would be able to do each simulation in just under an hour but now it looks like it will take the better part of two days, which is too much. I'll just have to run shorter or fewer simulations if I can't improve that, but I'm hoping I'm just doing something wrong. I'm essentially using modified versions of the .mdp file I found for this tutorial: http://www.alchemistry.org/wiki/GROMACS_4.6_example:_Direct_ethanol_solvation_free_energy. I changed things like turning off the pressure coupling, changing the temperature, etc. The settings for free energy calculations are unchanged. Is the calculation of dh/dl re ally that expensive, or is this abnormal? Thank you for the help as always. Regards, Nathan H. - Original Message - From: "Michael Shirts" To: "Discussion list for GROMACS users" Cc: "gromacs org gmx-users" Sent: Tuesday, October 6, 2015 3:05:38 PM Subject: Re: [gmx-users] Free Energy of Liquid Water For a pure fluid, G = N \mu. And \mu = (dG/dN)_(T,P). So you only need to change one molecule to ideal gas to get the change in free energy. The free energy of transfer of water from liquid to gas is indeed the free energy of solvation of one water molecule in bath of water. So there's a reason why you're just finding tutorials of solvation free energies! On Thu, Oct 1, 2015 at 10:44 PM, Nathan K Houtz wrote: > Hi everyone, > > I would like to use Gromacs to do Thermodynamic Integration (TI) from liquid > water (TIP4P model) to an ideal gas, to find the relative free energy. To do > this, I believe one generally integrates above the critical point by > increasing the temperature above the critical temperature and then relaxing > the pressure until the system is a diffuse gas. The mdp options documentation > is helpful, and I went through an ethanol solvation tutorial, but there > doesn't appear to be a "pressure-lambda" or a "volume-lambda" option that I > could use to do the second part. How can I get Gromacs to calculate the dh/dl > derivative while relaxing the pressure? > > In addition, all of the tutorials I found for thermodynamic integration were > for finding solvation free energies. The coulomb and VDW forces are > essentially changed from "completely on" to "completely off". But in my case, > I'd like to change the temperature and pressure between two nonzero values. I > don't want to begin my simulation at 0K and 0atm, but lambda *must* go from 0 > to 1. How can I define both starting and ending points for the temperature > and pressure (or volume, or density)? > > Thanks for your help! > Nathan H. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] pdb2gmx error
On 10/7/15 5:03 PM, Dries Van Rompaey wrote: Thanks Justin, that makes sense! I'm wondering why none of the other proline residues triggered that warning though? The same procedure works like a charm with other proteins. Without access to all of the files you're looking at, the best I can do is shrug my shoulders because that doesn't make any sense. Some prolines work and one doesn't? That's just not logical. -Justin On 7 Oct 2015 10:59 pm, "Justin Lemkul" wrote: On 10/7/15 3:01 PM, Dries Van Rompaey wrote: Hi Mark, This is Gromacs 5.0.4. This is a non-terminal residue. The command line used is: gmx pdb2gmx -f complex.pdb -o complex.gro (-ignh) I tried this procedure with and without ignh flag. As far as I know, specbonds is not in play. Non-terminal proline does not have an amide H. If your force field .rtp file claims to use such an atom used in a dihedral (which is what the error message tells you is happening), find out who altered the file and reprimand them :) -Justin Kind regards, Dries On 7 October 2015 at 20:56, Mark Abraham wrote: Hi, Is it terminal? Are there specbonds in play? What's the GROMACS version? What's your pdb2gmx command line? :-) Mark On Wed, Oct 7, 2015 at 8:43 PM Dries Van Rompaey < dries.vanromp...@gmail.com> wrote: Hi everyone, I'm getting the following warning when I try to run pdb2gmx on my protein structure: WARNING: WARNING: Residue 168 named PRO of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of type dihedral in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. This warning is only present when I use the AMBER03 forcefield, all other forcefields seem to work fine. I have tried this with both a structure without hydrogens as well as a structure with hydrogens added, both with and without the -ignh flag. I tried looking at the amber03 database files as well as the amber99sb-ildn database files (amber99sb-ildn works just fine), but I could not find any reason why this particular residue would be problematic. pdb2gmx does not find any problems with the other proline residues in the protein (which look identical), so I am puzzled as to what's causing this. The proline residue is: ATOM 1384 N PRO A 168 274.650 45.241 24.167 1.00180.63 N ATOM 1385 CA PRO A 168 273.508 44.823 23.370 1.00180.63 C ATOM 1386 CD PRO A 168 275.844 45.381 23.346 1.00180.63 C ATOM 1387 CB PRO A 168 274.071 44.405 22.014 1.00180.63 C ATOM 1388 CG PRO A 168 275.381 45.194 21.892 1.00180.63 C ATOM 1389 C PRO A 168 272.551 43.776 23.888 1.00180.63 C ATOM 1390 O PRO A 168 271.478 43.646 23.304 1.00180.63 O Does anyone know what's going on here? Thanks in advance! -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.
Re: [gmx-users] pdb2gmx error
Thanks Justin, that makes sense! I'm wondering why none of the other proline residues triggered that warning though? The same procedure works like a charm with other proteins. On 7 Oct 2015 10:59 pm, "Justin Lemkul" wrote: > > > On 10/7/15 3:01 PM, Dries Van Rompaey wrote: > >> Hi Mark, >> >> This is Gromacs 5.0.4. This is a non-terminal residue. >> The command line used is: >> gmx pdb2gmx -f complex.pdb -o complex.gro (-ignh) >> I tried this procedure with and without ignh flag. >> As far as I know, specbonds is not in play. >> >> > Non-terminal proline does not have an amide H. If your force field .rtp > file claims to use such an atom used in a dihedral (which is what the error > message tells you is happening), find out who altered the file and > reprimand them :) > > -Justin > > Kind regards, >> Dries >> >> >> On 7 October 2015 at 20:56, Mark Abraham >> wrote: >> >> Hi, >>> >>> Is it terminal? Are there specbonds in play? What's the GROMACS version? >>> What's your pdb2gmx command line? :-) >>> >>> Mark >>> >>> On Wed, Oct 7, 2015 at 8:43 PM Dries Van Rompaey < >>> dries.vanromp...@gmail.com> >>> wrote: >>> >>> Hi everyone, I'm getting the following warning when I try to run pdb2gmx on my protein structure: WARNING: WARNING: Residue 168 named PRO of a molecule in the input file >>> was >>> mapped to an entry in the topology database, but the atom H used in an interaction of type dihedral in that entry is not found in the input >>> file. >>> Perhaps your atom and/or residue naming needs to be fixed. This warning is only present when I use the AMBER03 forcefield, all other forcefields seem to work fine. I have tried this with both a structure without hydrogens as well as a structure with hydrogens added, both with and without the -ignh flag. I tried looking at the amber03 database files as well as the amber99sb-ildn database files (amber99sb-ildn works just fine), but I could not find any reason why this particular residue would >>> be >>> problematic. pdb2gmx does not find any problems with the other proline residues in the protein (which look identical), so I am puzzled as to what's causing this. The proline residue is: ATOM 1384 N PRO A 168 274.650 45.241 24.167 1.00180.63 N ATOM 1385 CA PRO A 168 273.508 44.823 23.370 1.00180.63 C ATOM 1386 CD PRO A 168 275.844 45.381 23.346 1.00180.63 C ATOM 1387 CB PRO A 168 274.071 44.405 22.014 1.00180.63 C ATOM 1388 CG PRO A 168 275.381 45.194 21.892 1.00180.63 C ATOM 1389 C PRO A 168 272.551 43.776 23.888 1.00180.63 C ATOM 1390 O PRO A 168 271.478 43.646 23.304 1.00180.63 O Does anyone know what's going on here? Thanks in advance! -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>> posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>> send a mail to gmx-users-requ...@gromacs.org. >>> >>> > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] pdb2gmx error
On 10/7/15 3:01 PM, Dries Van Rompaey wrote: Hi Mark, This is Gromacs 5.0.4. This is a non-terminal residue. The command line used is: gmx pdb2gmx -f complex.pdb -o complex.gro (-ignh) I tried this procedure with and without ignh flag. As far as I know, specbonds is not in play. Non-terminal proline does not have an amide H. If your force field .rtp file claims to use such an atom used in a dihedral (which is what the error message tells you is happening), find out who altered the file and reprimand them :) -Justin Kind regards, Dries On 7 October 2015 at 20:56, Mark Abraham wrote: Hi, Is it terminal? Are there specbonds in play? What's the GROMACS version? What's your pdb2gmx command line? :-) Mark On Wed, Oct 7, 2015 at 8:43 PM Dries Van Rompaey < dries.vanromp...@gmail.com> wrote: Hi everyone, I'm getting the following warning when I try to run pdb2gmx on my protein structure: WARNING: WARNING: Residue 168 named PRO of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of type dihedral in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. This warning is only present when I use the AMBER03 forcefield, all other forcefields seem to work fine. I have tried this with both a structure without hydrogens as well as a structure with hydrogens added, both with and without the -ignh flag. I tried looking at the amber03 database files as well as the amber99sb-ildn database files (amber99sb-ildn works just fine), but I could not find any reason why this particular residue would be problematic. pdb2gmx does not find any problems with the other proline residues in the protein (which look identical), so I am puzzled as to what's causing this. The proline residue is: ATOM 1384 N PRO A 168 274.650 45.241 24.167 1.00180.63 N ATOM 1385 CA PRO A 168 273.508 44.823 23.370 1.00180.63 C ATOM 1386 CD PRO A 168 275.844 45.381 23.346 1.00180.63 C ATOM 1387 CB PRO A 168 274.071 44.405 22.014 1.00180.63 C ATOM 1388 CG PRO A 168 275.381 45.194 21.892 1.00180.63 C ATOM 1389 C PRO A 168 272.551 43.776 23.888 1.00180.63 C ATOM 1390 O PRO A 168 271.478 43.646 23.304 1.00180.63 O Does anyone know what's going on here? Thanks in advance! -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] pdb2gmx error
Hi Mark, This is Gromacs 5.0.4. This is a non-terminal residue. The command line used is: gmx pdb2gmx -f complex.pdb -o complex.gro (-ignh) I tried this procedure with and without ignh flag. As far as I know, specbonds is not in play. Kind regards, Dries On 7 October 2015 at 20:56, Mark Abraham wrote: > Hi, > > Is it terminal? Are there specbonds in play? What's the GROMACS version? > What's your pdb2gmx command line? :-) > > Mark > > On Wed, Oct 7, 2015 at 8:43 PM Dries Van Rompaey < > dries.vanromp...@gmail.com> > wrote: > > > Hi everyone, > > > > I'm getting the following warning when I try to run pdb2gmx on my protein > > structure: > > > > WARNING: WARNING: Residue 168 named PRO of a molecule in the input file > was > > mapped to an entry in the topology database, but the atom H used in an > > interaction of type dihedral in that entry is not found in the input > file. > > Perhaps your atom and/or residue naming needs to be fixed. > > > > This warning is only present when I use the AMBER03 forcefield, all other > > forcefields seem to work fine. I have tried this with both a structure > > without hydrogens as well as a structure with hydrogens added, both with > > and without the -ignh flag. I tried looking at the amber03 database files > > as well as the amber99sb-ildn database files (amber99sb-ildn works just > > fine), but I could not find any reason why this particular residue would > be > > problematic. pdb2gmx does not find any problems with the other proline > > residues in the protein (which look identical), so I am puzzled as to > > what's causing this. > > > > The proline residue is: > > ATOM 1384 N PRO A 168 274.650 45.241 24.167 1.00180.63 > > N > > ATOM 1385 CA PRO A 168 273.508 44.823 23.370 1.00180.63 > > C > > ATOM 1386 CD PRO A 168 275.844 45.381 23.346 1.00180.63 > > C > > ATOM 1387 CB PRO A 168 274.071 44.405 22.014 1.00180.63 > > C > > ATOM 1388 CG PRO A 168 275.381 45.194 21.892 1.00180.63 > > C > > ATOM 1389 C PRO A 168 272.551 43.776 23.888 1.00180.63 > > C > > ATOM 1390 O PRO A 168 271.478 43.646 23.304 1.00180.63 > > O > > > > Does anyone know what's going on here? > > > > Thanks in advance! > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] pdb2gmx error
Hi, Is it terminal? Are there specbonds in play? What's the GROMACS version? What's your pdb2gmx command line? :-) Mark On Wed, Oct 7, 2015 at 8:43 PM Dries Van Rompaey wrote: > Hi everyone, > > I'm getting the following warning when I try to run pdb2gmx on my protein > structure: > > WARNING: WARNING: Residue 168 named PRO of a molecule in the input file was > mapped to an entry in the topology database, but the atom H used in an > interaction of type dihedral in that entry is not found in the input file. > Perhaps your atom and/or residue naming needs to be fixed. > > This warning is only present when I use the AMBER03 forcefield, all other > forcefields seem to work fine. I have tried this with both a structure > without hydrogens as well as a structure with hydrogens added, both with > and without the -ignh flag. I tried looking at the amber03 database files > as well as the amber99sb-ildn database files (amber99sb-ildn works just > fine), but I could not find any reason why this particular residue would be > problematic. pdb2gmx does not find any problems with the other proline > residues in the protein (which look identical), so I am puzzled as to > what's causing this. > > The proline residue is: > ATOM 1384 N PRO A 168 274.650 45.241 24.167 1.00180.63 > N > ATOM 1385 CA PRO A 168 273.508 44.823 23.370 1.00180.63 > C > ATOM 1386 CD PRO A 168 275.844 45.381 23.346 1.00180.63 > C > ATOM 1387 CB PRO A 168 274.071 44.405 22.014 1.00180.63 > C > ATOM 1388 CG PRO A 168 275.381 45.194 21.892 1.00180.63 > C > ATOM 1389 C PRO A 168 272.551 43.776 23.888 1.00180.63 > C > ATOM 1390 O PRO A 168 271.478 43.646 23.304 1.00180.63 > O > > Does anyone know what's going on here? > > Thanks in advance! > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] pdb2gmx error
Hi everyone, I'm getting the following warning when I try to run pdb2gmx on my protein structure: WARNING: WARNING: Residue 168 named PRO of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of type dihedral in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. This warning is only present when I use the AMBER03 forcefield, all other forcefields seem to work fine. I have tried this with both a structure without hydrogens as well as a structure with hydrogens added, both with and without the -ignh flag. I tried looking at the amber03 database files as well as the amber99sb-ildn database files (amber99sb-ildn works just fine), but I could not find any reason why this particular residue would be problematic. pdb2gmx does not find any problems with the other proline residues in the protein (which look identical), so I am puzzled as to what's causing this. The proline residue is: ATOM 1384 N PRO A 168 274.650 45.241 24.167 1.00180.63 N ATOM 1385 CA PRO A 168 273.508 44.823 23.370 1.00180.63 C ATOM 1386 CD PRO A 168 275.844 45.381 23.346 1.00180.63 C ATOM 1387 CB PRO A 168 274.071 44.405 22.014 1.00180.63 C ATOM 1388 CG PRO A 168 275.381 45.194 21.892 1.00180.63 C ATOM 1389 C PRO A 168 272.551 43.776 23.888 1.00180.63 C ATOM 1390 O PRO A 168 271.478 43.646 23.304 1.00180.63 O Does anyone know what's going on here? Thanks in advance! -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] GROMACS On GPU
Hi, Check out what the install guide says ;-) Mark On Wed, Oct 7, 2015 at 3:43 PM Nikhil wrote: > only i need to install from source,or should i install CUDA Toolkit? > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] installing gromacs-5.0.5
i think you should install by downloading source file and CUDA toolkit for your GPU.may i know what is your GPU? i also wondering about GPU and CUDA ? Nikhil -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Gromacs
Hi, How is it possible that you have finished up to production run without the .top file ? The first line of your ebolaag.top says that the topology has been generated. How have you been doing any of the equilibration steps without the .top file? Information regarding atoms are there in the ebolaag_Protein_chain_A.itp and the ebolaag_Ion_chain_A2.itp files created by pdb2gmx. Your comments do not make any sense to me. Soumadwip -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Install Gromacs on VirtualBox
Hi, Unfortunately that does not tell much (at least not without a backtrace). You can e.g. run the regressiontests to see whether mdrun does start at all (or just run "gmx mdrun" manually). -- Szilárd On Tue, Oct 6, 2015 at 4:06 PM, Simon Dürr wrote: > Hi Szilard, > > thanks for the help. Now only 1 of 15 tests fails. > > > Label Time Summary: > > GTest = 4.92 sec > > IntegrationTest= 4.05 sec > > UnitTest = 4.92 sec > > Total Test time (real) = 9.18 sec > > The following tests FAILED: > > 15 - MdrunTests (SEGFAULT) > > Errors while running CTest > > make[3]: *** [CMakeFiles/run-ctest] Error 8 > > make[2]: *** [CMakeFiles/run-ctest.dir/all] Error 2 > > make[1]: *** [CMakeFiles/check.dir/rule] Error 2 > > make: *** [check] Error 2 > > See CMakeCache.txt here: http://pastebin.com/u4xwQcar > > 2015-10-05 11:29 GMT-04:00 Szilárd Páll : > > Oh, that was easy, should have asked about what the value of "GMX_SIMD" > is > > in the CMake cache. Given that the GROMACS build system enabled AVX2 SIMD > > on your VM which seems to not support anything above SSE2, it's not a > > surprise that the first math instruction crashes the run. > > > > Immediate solution: set -DGMX_SIMD=SSE2 when configuring. > > > > Secondly: please open an issue on redmine.gromacs.org and briefly > summarize > > what you described here (+ the VM setup you have) and attach the > > /proc/cpuinfo and CMakeCache.txt so we can have a look at why is the > build > > system picking AVX2 even though the virtualized CPU does not support it. > > > > Thanks, > > > > -- > > Szilárd > > > > On Sun, Oct 4, 2015 at 4:04 AM, Simon Dürr > > wrote: > > > >> After running make check I can install via sudo make install. > >> gmx --version returns: > >> http://pastebin.com/Gnx09wah > >> > >> The CMakeCache file is the following: > >> http://pastebin.com/9wb0e1tw > >> > >> Cheers, > >> Simon > >> > >> 2015-10-02 17:58 GMT-04:00 Szilárd Páll : > >> > Should have asked for the CMakeCache file too, could you post that to > a > >> > file sharing service? > >> > > >> > If you happen to have GMX_SIMD other than SSE2, that would explain the > >> > issue - although I can't imagine why would the instruction set > detection > >> > fail. > >> > > >> > Do you get an "illegal instruction" error if you e.g. try to run "gmx > >> > -version" from the build tree? > >> > > >> > Cheers, > >> > > >> > -- > >> > Szilárd > >> > > >> > On Fri, Oct 2, 2015 at 11:12 PM, Simon Dürr < > simon.du...@uni-konstanz.de > >> > > >> > wrote: > >> > > >> >> Sure. > >> >> > >> >> >cat /proc/cpuinfo > >> >> > > >> >> > processor : 0 > >> >> > vendor_id : GenuineIntel > >> >> > cpu family : 6 > >> >> > model : 69 > >> >> > model name : Intel(R) Core(TM) i7-4550U CPU @ 1.50GHz > >> >> > stepping : 1 > >> >> > microcode : 0x19 > >> >> > cpu MHz : 2095.205 > >> >> > cache size : 6144 KB > >> >> > physical id : 0 > >> >> > siblings : 1 > >> >> > core id : 0 > >> >> > cpu cores : 1 > >> >> > apicid : 0 > >> >> > initial apicid : 0 > >> >> > fdiv_bug : no > >> >> > f00f_bug : no > >> >> > coma_bug : no > >> >> > fpu : yes > >> >> > fpu_exception : yes > >> >> > cpuid level : 5 > >> >> > wp : yes > >> >> > flags : fpu vme de pse tsc msr pae mce cx8 apic mtrr pge mca cmov > pat > >> >> pse36 clflush mmx fxsr sse sse2 rdtscp constant_tsc pni monitor ssse3 > >> >> > bugs : > >> >> > bogomips : 4190.41 > >> >> > clflush size : 64 > >> >> > cache_alignment : 64 > >> >> > address sizes : 39 bits physical, 48 bits virtual > >> >> > >> >> Cheers, > >> >> Simon > >> >> > >> >> 2015-10-02 5:36 GMT-04:00 Szilárd Páll : > >> >> > Hi, > >> >> > > >> >> > Can you share the CPUID flags shown in /proc/cpuinfo? > >> >> > > >> >> > > >> >> > -- > >> >> > Szilárd > >> >> > > >> >> > On Thu, Oct 1, 2015 at 7:03 PM, Simon Dürr < > >> simon.du...@uni-konstanz.de> > >> >> > wrote: > >> >> > > >> >> >> I used this: > >> >> >> > >> >> >> > cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=OFF > >> >> >> -DGMX_USE_RDTSCP=OFF > >> >> >> > >> >> >> But Still: > >> >> >> Test project /home/simon/gromacs-5.0.6/build > >> >> >> Start 1: TestUtilsUnitTests > >> >> >> 1/15 Test #1: TestUtilsUnitTests ...***Exception: > >> >> >> Illegal 0.29 sec > >> >> >> > >> >> >> Start 2: PreprocessingTests > >> >> >> 2/15 Test #2: PreprocessingTests ...***Exception: > >> >> >> Illegal 0.23 sec > >> >> >> > >> >> >> Start 3: CommandLineUnitTests > >> >> >> 3/15 Test #3: CommandLineUnitTests .***Exception: > >> >> >> Illegal 0.36 sec > >> >> >> > >> >> >> Start 4: FFTUnitTests > >> >> >> 4/15 Test #4: FFTUnitTests .***Exception: > >> >> >> Illegal 0.32 sec > >> >> >> > >> >> >> Start 5: RandomUnitTests > >> >> >> 5/15 Test #5: RandomUnitTests ..***Exception: > >> >> >> Illegal 0.25 sec > >> >> >> > >> >> >> Start 6: OnlineHelpUnitTests > >> >> >> 6/15 Test #6: OnlineHelpUnitTests
Re: [gmx-users] GROMACS On GPU
only i need to install from source,or should i install CUDA Toolkit? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Hydrogen bonding energy calculation (Ben)
Hi Dr. Spoel, Thanks for your reply! I set my script as follows: gmx pdb2gmx -f water.pdb -o water.gro -water tip3p << EOF #water.pdb is a pdb file contains a single water molecule 5 #OPLS 2 #TIP3P EOF gmx editconf -f water.gro -o water_newbox.gro -c -d 1.5 -bt cubic gmx solvate -cp water_newbox.gro -cs spc216.gro -o water_solv.gro -p topol.top gmx grompp -f em.mdp -c water_solv.gro -p topol.top -o em.tpr gmx mdrun -v -deffnm em gmx grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr gmx mdrun -deffnm nvt gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o npt.tpr gmx mdrun -deffnm npt gmx grompp -f md1.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr #a short 200 ps run gmx mdrun -deffnm md_0_1 gmx grompp -f md2.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_2.tpr #a longer 2 ns run gmx mdrun -deffnm md_0_2 gmx trjconv -s md_0_2.tpr -f md_0_2.trr -o md_0_2_noPBC.trr -pbc mol -ur compact << EOF 2 #SOL (water) EOF gmx hbond -f md_0_2_noPBC.trr -s md_0_2.tpr -num hbnum.xvg -temp 298.15 -ac hbac.xvg << EOF 2 #SOL (water) 2 #SOL (water) EOF Here is the specification of my md*.mdp file ; Run parameter integrator = md ; leap-frog integrator dt = 0.002; ps ! nsteps = 100 ; total 2 ns ; Output control nstxout = 50 ; save coordinates every 100 fs nstvout = 0 nstenergy = 50 ; save energy every 100 fs nstlog = 50 ; Bond parameters continuation= yes constraint_algorithm = SHAKE shake-tol = 0.0001 constraints = all-bonds ; Neighborsearching cutoff-scheme = Verlet ns_type = grid nstlist = 5 rcoulomb= 1.0 rvdw= 1.0 ; Electrostatics coulombtype = PME pme_order = 4 fourierspacing = 0.16 ; Temperature coupling is on Tcoupl = berendsen tc-grps = SOL tau_t = 0.1 ref_t = 298.15 ; Isotropic pressure coupling is now on Pcoupl = berendsen Pcoupltype = isotropic compressibility = 4.5e-5 tau_p = 1.0 ref_p = 1.0 refcoord_scaling= com ; Periodic boundary conditions pbc = xyz ; Dispersion correction DispCorr= EnerPres gen_vel = no Could you take a look at my parameters and script and let me know if there is anything that might cause the deviation? Thanks!! Ben -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Gromacs
Respected Sir, Though im finshed upto production step of protein metal complexes, topology file couldnt be created and there is no information about any atoms in my pdb file. the created topology file are shown below ; ;File 'ebolaag.top' was generated ;By user: onbekend (0) ;On host: onbekend ;At date: Wed Oct 7 16:06:22 2015 ; ;This is a standalone topology file ; ;It was generated using program: ;pdb2gmx_d - VERSION 4.5 ; ;Command line was: ;./pdb2gmx_d -f ebolaag.pdb -o ebolaag.gro -p ebolaag.top -ignh ; ;Force field was read from the standard Gromacs share directory. ; ; Include forcefield parameters #include "oplsaa.ff/forcefield.itp" ; Include chain topologies #include "ebolaag_Protein_chain_A.itp" #include "ebolaag_Ion_chain_A2.itp" ; Include water topology #include "oplsaa.ff/tip4p.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include "oplsaa.ff/ions.itp" [ system ] ; Name Protein in water [ molecules ] ; Compound#mols Protein_chain_A 1 Ion_chain_A21 SOL 4673 I can't understand what is the problem, so pls tell me what could be the reason for this. Sincierly, *Saranya Vasudevan,* *Research Scholar,* *Molecular Quantum Mechanics Laboratory,* *Department of Physics,* *Bharathiar University,* *Coimbatore-46* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Virtual sites error
Trying to add hydrogen virtual sites to the model (using -vsites h option in pdb2gmx) results in a salvo of error messages when running grommp to create .tpr file after the solvation: ERROR 1 [file topol_DNA_chain_A2.itp, line 1033]: No default Constr. No Conn. types ERROR 2 [file topol_DNA_chain_A2.itp, line 1034]: No default Constr. No Conn. types This lines in constraints section in the .itp file refer to pairs of two MCH3 and one MC atoms, which should serve (the way I understand the situation) as replacement methyl group in thymine. There are several more pairs of same errors corresponding to different thymine methyl groups in the DNA strands. Here is the relevant sections of the itp file for the first two errors: [ constraints ] ; aiaj functc0c1 2 3 2 110 111 2 110 112 2 111 112 2 [ atoms ] 110 CM321 DT C5110 0.0025 12.01 ; qtot -2.867 111 MCH3321 DT MC71111 0 7.517 ; qtot -2.867 112 MCH3321 DT MC72111 0 7.517 ; qtot -2.867 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Gromacs
i tried to run in OPLSAA force field sir. *Saranya Vasudevan,* *Research Scholar,* *Molecular Quantum Mechanics Laboratory,* *Department of Physics,* *Bharathiar University,* *Coimbatore-46* On Tue, Oct 6, 2015 at 7:39 PM, Ebert Maximilian wrote: > Maybe you should start telling is which force field you are trying to use. > GROMACS provides 15 different. > > Max > > > On Oct 6, 2015, at 1:51 AM, saranya wrote: > > > > GROMACS users, > > > > I was trying to perform a MD simulation of a system with a protein with > Ag+ > > metal ion but realized that GROMACS does not have parameters for the Ag+ > > ion. I tried to include the parameters in the ion.itp file but did not > > succeed yet. Does anyone knows the right procedure to introduce this ions > > into the file ions.itp? do we have to change anything more in order to > > GROMACS recognize the new ion? > > > > With Regards > > > > *Saranya Vasudevan,* > > > > *Research Scholar,* > > > > *Molecular Quantum Mechanics Laboratory,* > > > > *Department of Physics,* > > > > *Bharathiar University,* > > > > *Coimbatore-46* > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
