[gmx-users] Different force constants for different umbrella windows?
Dear GROMACS users, I've a question regarding umbrella sampling and its evaluation with gmx wham. Is it possible to use different force constants for different umbrella windows? Thanks, Andreas -- M. Sc. Andreas Mecklenfeld Technische Universität Braunschweig Institut für Thermodynamik Hans-Sommer-Straße 5 38106 Braunschweig Deutschland / Germany Tel: +49 (0)531 391-2634 +49 (0)531 391-65685 Fax: +49 (0)531 391-7814 https://www.tu-braunschweig.de/ift https://www.tu-braunschweig.de/ift/agmolth -- 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] PMF in inhomogeneous fluid phase
Dear Gromacs-users, I have a question that may not be directly Gromacs-related. I want to calculate the potential of mean force (PMF) for a solute that is pulled away from a crystal surface. The issue is that the fluid phase is inhomogeneous, as it consists of water and cluster-forming ions. From my understanding, this would make the PMF calculation not only dependent on the pull-coordinate (z-axis of the simulation box), but the PMF would be also influenced by the position of the clusters which might change their position randomly in different umbrella windows. One could restrain the positions of the ions to freeze the local composition. However, this would be an enormous interference into the system and I'm not really comfortable in doing so. Any suggestions would be highly appreciated. Bests, Andreas -- M. Sc. Andreas Mecklenfeld Technische Universität Braunschweig Institut für Thermodynamik Hans-Sommer-Straße 5 38106 Braunschweig Deutschland / Germany Tel: +49 (0)531 391-2634 +49 (0)531 391-65685 Fax: +49 (0)531 391-7814 https://www.tu-braunschweig.de/ift https://www.tu-braunschweig.de/ift/agmolth -- 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] Number of bins for wham and umbrella sampling / PMF
Dear Gromacs users, I want to perform umbrella sampling in order to calculate the PMF for pulling a molecule from a surface. For evaluation, I use gmx wham with bootstrapping, and Gromacs version is 2018.4. I've noticed that my results strongly depend on the number of bins, with peak heights differ in the magnitude of several kJ/mol. The histograms display reasonable overlap. I've tried to alter the number of bins to search for convergence (starting from default 200, I used up to 1 bins), though convergence was not achieved. Is this an expected behaviour and is the default 200 a suitable number of bins? Thanks, Andreas -- M. Sc. Andreas Mecklenfeld Technische Universität Braunschweig Institut für Thermodynamik Hans-Sommer-Straße 5 38106 Braunschweig Deutschland / Germany Tel: +49 (0)531 391-2634 +49 (0)531 391-65685 Fax: +49 (0)531 391-7814 http://www.ift-bs.de -- 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] combine -rerun and -multi features of mdrun
Dear Gromacs users, I would like to combine the -rerun with the -multi feature of the mdrun command. For the -multi feature, I understand that I have to rename my input files to e.g. system0.tpr, system1.tpr, ... - correct? I would like to interpret energies for these systems, based on the same trajectory file. Is it possible to refer to the trajetory file as e.g. system*.trr, so that I don't have to duplicate and rename the files to system0.trr, system1.trr etc.? Thanks and regards, Andreas -- M. Sc. Andreas Mecklenfeld Technische Universität Braunschweig Institut für Thermodynamik Hans-Sommer-Straße 5 38106 Braunschweig Deutschland / Germany Tel: +49 (0)531 391-2634 +49 (0)531 391-65685 Fax: +49 (0)531 391-7814 http://www.ift-bs.de -- 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] gmx mdrun -rerun issue
Dear Benson, thanks for the offer. I've used gmx traj to generate a smaller *.trr file, though the occuring issue seems unaffected. I've uploaded my files to http://ge.tt/1HNpO8s2 Kind regards, Andreas Am 09.10.2018 um 10:48 schrieb Benson Muite: Current version 2018.3 seems to have re-run feature: http://manual.gromacs.org/documentation/current/user-guide/mdrun-features.html Is your input data reasonable? Might a small version be available where one could try this in 2018.3 to see if the same error is obtained? Benson On 10/9/18 11:40 AM, Andreas Mecklenfeld wrote: Hey, thanks for the quick response. Unfortunately, there isn't (at least not in the short-term). Which one would be suitable though? Best regards, Andreas Am 09.10.2018 um 10:31 schrieb Benson Muite: Hi, Is it possible to use a newer version of Gromacs? Benson On 10/9/18 11:15 AM, Andreas Mecklenfeld wrote: Dear Gromacs users, I've a question regarding the rerun option of the mdrun command in Gromacs 2016.1. It seems as if the calculation is repeatedly performed for the last frame (until killed by the work station). The output is "Last frame 1000 time 2000.000 WARNING: Incomplete header: nr 1001 time 2000" My goal is to alter the .top-file (new) and calculate energies with previously recorded coordinates (old): "gmx grompp -f old_PROD.mdp -c old_PROD.gro -p new_topol.top -o new_PROD.tpr" The mdrun looks like "gmx mdrun -rerun old_PROD.trr -deffnm new_PROD" Is there a way to fix this? Thanks, Andreas -- M. Sc. Andreas Mecklenfeld Technische Universität Braunschweig Institut für Thermodynamik Hans-Sommer-Straße 5 38106 Braunschweig Deutschland / Germany Tel: +49 (0)531 391-2634 +49 (0)531 391-65685 Fax: +49 (0)531 391-7814 http://www.ift-bs.de -- 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] gmx mdrun -rerun issue
Hey, thanks for the quick response. Unfortunately, there isn't (at least not in the short-term). Which one would be suitable though? Best regards, Andreas Am 09.10.2018 um 10:31 schrieb Benson Muite: Hi, Is it possible to use a newer version of Gromacs? Benson On 10/9/18 11:15 AM, Andreas Mecklenfeld wrote: Dear Gromacs users, I've a question regarding the rerun option of the mdrun command in Gromacs 2016.1. It seems as if the calculation is repeatedly performed for the last frame (until killed by the work station). The output is "Last frame 1000 time 2000.000 WARNING: Incomplete header: nr 1001 time 2000" My goal is to alter the .top-file (new) and calculate energies with previously recorded coordinates (old): "gmx grompp -f old_PROD.mdp -c old_PROD.gro -p new_topol.top -o new_PROD.tpr" The mdrun looks like "gmx mdrun -rerun old_PROD.trr -deffnm new_PROD" Is there a way to fix this? Thanks, Andreas -- M. Sc. Andreas Mecklenfeld Technische Universität Braunschweig Institut für Thermodynamik Hans-Sommer-Straße 5 38106 Braunschweig Deutschland / Germany Tel: +49 (0)531 391-2634 +49 (0)531 391-65685 Fax: +49 (0)531 391-7814 http://www.ift-bs.de -- 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] gmx mdrun -rerun issue
Dear Gromacs users, I've a question regarding the rerun option of the mdrun command in Gromacs 2016.1. It seems as if the calculation is repeatedly performed for the last frame (until killed by the work station). The output is "Last frame 1000 time 2000.000 WARNING: Incomplete header: nr 1001 time 2000" My goal is to alter the .top-file (new) and calculate energies with previously recorded coordinates (old): "gmx grompp -f old_PROD.mdp -c old_PROD.gro -p new_topol.top -o new_PROD.tpr" The mdrun looks like "gmx mdrun -rerun old_PROD.trr -deffnm new_PROD" Is there a way to fix this? Thanks, Andreas -- M. Sc. Andreas Mecklenfeld Technische Universität Braunschweig Institut für Thermodynamik Hans-Sommer-Straße 5 38106 Braunschweig Deutschland / Germany Tel: +49 (0)531 391-2634 +49 (0)531 391-65685 Fax: +49 (0)531 391-7814 http://www.ift-bs.de -- 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] gmx energy: error estimate?
Dear GROMACS-users, I've a question regarding the gmx energy command. In the online manual it says "An error estimate of the average is given based on a block averages over 5 blocks using the full-precision averages.". How exactly is the error estimate calculated? Thanks and regards Andreas -- M. Sc. Andreas Mecklenfeld Stipendiat Technische Universität Braunschweig Institut für Thermodynamik Hans-Sommer-Straße 5 38106 Braunschweig Deutschland / Germany Tel: +49 (0)531 391-2634 Fax: +49 (0)531 391-7814 http://www.ift-bs.de -- 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] Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)
Dear Mark and Justin, I've switched to function type 1 and the simulation runs. I thought the function type would correspond to the type of the comb-rule and missed the information given in the 5.8.1 section of the manual. Thanks a lot! Andreas Am 12.08.2016 um 14:15 schrieb Justin Lemkul: On 8/12/16 8:11 AM, Andreas Mecklenfeld wrote: Hello Mark, sorry for the confusion I've created. My system refers to a solute in water (which has only LJ-parameters for the oxygen atom). Within the solute, there are two approaches to deal with LJ-interactions: 1) intramolecular interactions (including 1-4 and far-off interactions) 2) intermolecular interactions with the oxygens of ambient water There are certain atom types, which handle points 1) and 2) with different sets of LJ-parameters. Since the water oxygen is not included within the solute topology, the pair potential between the affected solute atomtype and the water-oxygen atomtype therefore has to be intermolecular. My .top file looks like this: # [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 0.5 0.8333 [ atomtypes ] ;name bond_type mass charge ptype sigma epsilon Amb o3 o3 0.0 0.0 A 2.95992e-01 8.78640e-01 ; 1.66 0.2100 oa oa 0.0 0.0 A 3.06647e-01 8.80314e-01 ; 1.72 0.2104 od od 0.0 0.0 A 2.95992e-01 8.78640e-01 ; 1.66 0.2100 nd nd 0.0 0.0 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 nl nl 0.0 0.0 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 sh sh 0.0 0.0 A 3.56359e-01 1.04600e+00 ; 2.00 0.2500 o3i o3i 0.0 0.0 A 0.331503 0.878640; 1.66 0.2100 oai oai 0.0 0.0 A 0.295778 0.880314; 1.72 0.2104 odi odi 0.0 0.0 A 0.320724 0.878640; 1.66 0.2100 ndi ndi 0.0 0.0 A 0.349232 0.711280; 1.82 0.1700 nli nli 0.0 0.0 A 0.299003 0.711280; 1.82 0.1700 shi shi 0.0 0.0 A 0.334978 1.046000; 2.00 0.2500 c3 c3 0.0 0.0 A 3.39967e-01 4.57730e-01 ; 1.91 0.1094 hc hc 0.0 0.0 A 2.64953e-01 6.56888e-02 ; 1.49 0.0157 cc 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 oo 0.0 0.0 A 2.95992e-01 8.78640e-01 ; 1.66 0.2100 nn 0.0 0.0 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 hn hn 0.0 0.0 A 1.06908e-01 6.56888e-02 ; 0.60 0.0157 cc cc 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 cd cd 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 h4 h4 0.0 0.0 A 2.51055e-01 6.27600e-02 ; 1.41 0.0150 h5 h5 0.0 0.0 A 2.42146e-01 6.27600e-02 ; 1.36 0.0150 na na 0.0 0.0 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 h1 h1 0.0 0.0 A 2.47135e-01 6.56888e-02 ; 1.39 0.0157 ss ss 0.0 0.0 A 3.56359e-01 1.04600e+00 ; 2.00 0.2500 ca ca 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 ha ha 0.0 0.0 A 2.59964e-01 6.27600e-02 ; 1.46 0.0150 oh oh 0.0 0.0 A 3.06647e-01 8.80314e-01 ; 1.72 0.2104 ho ho 0.0 0.0 A 0.0e+00 0.0e+00 ; 0.00 0. HW_tip4pew 1 1.008 0. A 0.0e+00 0.0e+00 OW_tip4pew 8 16.000. A 3.16435e-01 6.80946e-01 MW 0 0. 0. D 0.0e+00 0.0e+00 [ nonbond_params ] OW_tip4pewo3i2 0.3239690.773503 OW_tip4pewoai2 0.3061070.774239 OW_tip4pewodi2 0.3185790.773503 OW_tip4pewndi2 0.3328340.695948 OW_tip4pewnli2 0.3077190.695948 OW_tip4pewshi2 0.3257060.843961 #include "Asn.itp" #include "tip4pew.itp" [ system ] Asn in tip4pew [ molecules ] ; molecule namenr. Asn1 SOL900 # When I comment out the [ non_bond_params ] section, everything works fine, thus I would locate the error to this point. The error I receive is actually the one from the mail subject: ERROR 1 [file topol.top, line 44]: Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR) followed by repetitions regarding the other lines in the [ non_bond_params ]
Re: [gmx-users] Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)
Hello Mark, sorry for the confusion I've created. My system refers to a solute in water (which has only LJ-parameters for the oxygen atom). Within the solute, there are two approaches to deal with LJ-interactions: 1) intramolecular interactions (including 1-4 and far-off interactions) 2) intermolecular interactions with the oxygens of ambient water There are certain atom types, which handle points 1) and 2) with different sets of LJ-parameters. Since the water oxygen is not included within the solute topology, the pair potential between the affected solute atomtype and the water-oxygen atomtype therefore has to be intermolecular. My .top file looks like this: # [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 0.5 0.8333 [ atomtypes ] ;name bond_type mass charge ptype sigma epsilon Amb o3 o3 0.0 0.0 A 2.95992e-01 8.78640e-01 ; 1.66 0.2100 oa oa 0.0 0.0 A 3.06647e-01 8.80314e-01 ; 1.72 0.2104 od od 0.0 0.0 A 2.95992e-01 8.78640e-01 ; 1.66 0.2100 nd nd 0.0 0.0 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 nl nl 0.0 0.0 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 sh sh 0.0 0.0 A 3.56359e-01 1.04600e+00 ; 2.00 0.2500 o3i o3i 0.0 0.0 A 0.331503 0.878640; 1.66 0.2100 oai oai 0.0 0.0 A 0.295778 0.880314; 1.72 0.2104 odi odi 0.0 0.0 A 0.320724 0.878640; 1.66 0.2100 ndi ndi 0.0 0.0 A 0.349232 0.711280; 1.82 0.1700 nli nli 0.0 0.0 A 0.299003 0.711280; 1.82 0.1700 shi shi 0.0 0.0 A 0.334978 1.046000; 2.00 0.2500 c3 c3 0.0 0.0 A 3.39967e-01 4.57730e-01 ; 1.91 0.1094 hc hc 0.0 0.0 A 2.64953e-01 6.56888e-02 ; 1.49 0.0157 cc 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 oo 0.0 0.0 A 2.95992e-01 8.78640e-01 ; 1.66 0.2100 nn 0.0 0.0 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 hn hn 0.0 0.0 A 1.06908e-01 6.56888e-02 ; 0.60 0.0157 cc cc 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 cd cd 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 h4 h4 0.0 0.0 A 2.51055e-01 6.27600e-02 ; 1.41 0.0150 h5 h5 0.0 0.0 A 2.42146e-01 6.27600e-02 ; 1.36 0.0150 na na 0.0 0.0 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 h1 h1 0.0 0.0 A 2.47135e-01 6.56888e-02 ; 1.39 0.0157 ss ss 0.0 0.0 A 3.56359e-01 1.04600e+00 ; 2.00 0.2500 ca ca 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 ha ha 0.0 0.0 A 2.59964e-01 6.27600e-02 ; 1.46 0.0150 oh oh 0.0 0.0 A 3.06647e-01 8.80314e-01 ; 1.72 0.2104 ho ho 0.0 0.0 A 0.0e+00 0.0e+00 ; 0.00 0. HW_tip4pew 1 1.008 0. A 0.0e+00 0.0e+00 OW_tip4pew 8 16.000. A 3.16435e-01 6.80946e-01 MW 0 0. 0. D 0.0e+00 0.0e+00 [ nonbond_params ] OW_tip4pewo3i2 0.3239690.773503 OW_tip4pewoai2 0.3061070.774239 OW_tip4pewodi2 0.3185790.773503 OW_tip4pewndi2 0.3328340.695948 OW_tip4pewnli2 0.3077190.695948 OW_tip4pewshi2 0.3257060.843961 #include "Asn.itp" #include "tip4pew.itp" [ system ] Asn in tip4pew [ molecules ] ; molecule namenr. Asn1 SOL900 # When I comment out the [ non_bond_params ] section, everything works fine, thus I would locate the error to this point. The error I receive is actually the one from the mail subject: ERROR 1 [file topol.top, line 44]: Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR) followed by repetitions regarding the other lines in the [ non_bond_params ] section. Thanks for your help! Andreas Am 12.08.2016 um 09:49 schrieb Mark Abraham: Hi, On Fri, Aug 12, 2016 at 9:16 AM Andreas Mecklenfeld < a.mecklenf...@tu-braunschweig.de> wrote: Hello Mark, thanks for the reply. The point is, I don't. Ah, I read your original email more closely now. The use of a subject line that reflected your
Re: [gmx-users] Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)
Hello Mark, thanks for the reply. The point is, I don't. I found some Lennard-Jones parametrization in literature that distinguishes between intra- and intermolecular (oxygen atom of water) interactions. My intention was thus to define the specific eps_ij and sigma_ij for the corresponding atomtypes, which I thought should be dealt with in the [ nonbond_params ] section. All parameters are for Lennard-Jones and this is the potential I want to use. I have no idea why the usage of Buckingham is assumed. I'm using Gromacs 5.1 btw. Thanks, Andreas Am 11.08.2016 um 17:59 schrieb Mark Abraham: Hi, How do you want your atoms with lj parameters to interact with atoms with Buckingham parameters? Mark On Fri, 5 Aug 2016 08:53 Andreas Mecklenfeld < a.mecklenf...@tu-braunschweig.de> wrote: Dear Gromacs-users, I'm trying to modify some intermolecular Lennard-Jones interactions based on the GAFF force field. I've altered the topology file according to [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 0.5 0.8333 [ atomtypes ] ... [ nonbond_params ] type1type2sigmaepsilon ... #include ... [ system ] ... [ molecules ] ... Sigma and epsilon for atoms type1 and type2 are calculated according to the Lorentz-Berthelot combination rule. The error I receive is "Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)", though I obviously want to use LJ and did not intentionally set any flag for Buckingham. Is there any way to fix this? Cheers, Andreas -- M. Sc. Andreas Mecklenfeld Stipendiat Technische Universität Braunschweig Institut für Thermodynamik Hans-Sommer-Straße 5 38106 Braunschweig Deutschland / Germany Tel: +49 (0)531 391-2634 Fax: +49 (0)531 391-7814 http://www.ift-bs.de -- 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. -- M. Sc. Andreas Mecklenfeld Stipendiat Technische Universität Braunschweig Institut für Thermodynamik Hans-Sommer-Straße 5 38106 Braunschweig Deutschland / Germany Tel: +49 (0)531 391-2634 Fax: +49 (0)531 391-7814 http://www.ift-bs.de -- 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] Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)
Dear Gromacs-users, I'm trying to modify some intermolecular Lennard-Jones interactions based on the GAFF force field. I've altered the topology file according to [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 0.5 0.8333 [ atomtypes ] ... [ nonbond_params ] type1type2sigmaepsilon ... #include ... [ system ] ... [ molecules ] ... Sigma and epsilon for atoms type1 and type2 are calculated according to the Lorentz-Berthelot combination rule. The error I receive is "Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)", though I obviously want to use LJ and did not intentionally set any flag for Buckingham. Is there any way to fix this? Cheers, Andreas -- M. Sc. Andreas Mecklenfeld Stipendiat Technische Universität Braunschweig Institut für Thermodynamik Hans-Sommer-Straße 5 38106 Braunschweig Deutschland / Germany Tel: +49 (0)531 391-2634 Fax: +49 (0)531 391-7814 http://www.ift-bs.de -- 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] Gromacs 5.1 I/O strategy
Dear Gromacs-users, I'm currently working on a project proposal to acquire computational time. For this, I have to specify the I/O strategy used in Gromacs 5.1. Unfortunately, I found very little information about this topic. By analyzing my log-files, it seems that all (12) MPI ranks participate in writing the trajectory. Does this apply for the other data as well? Can you link me to further material / references? Thanks & regards, Andreas -- M. Sc. Andreas Mecklenfeld Stipendiat Technische Universität Braunschweig Institut für Thermodynamik Hans-Sommer-Straße 5 38106 Braunschweig Deutschland / Germany Tel: +49 (0)531 391-2634 Fax: +49 (0)531 391-7814 http://www.ift-bs.de -- 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] Free energy including change in temperature
Dear Gromacs users, I would like to try a free energy calculation including a change in temperature using the temperature-lambdas-vector. It says in the online manual that each entry has to be between 0 and 1. How can I define the corresponding temperatures (something like couple-lambda0 / couple-lambda1)? Thanks & regards, Andreas -- M. Sc. Andreas Mecklenfeld Stipendiat Technische Universität Braunschweig Institut für Thermodynamik Hans-Sommer-Straße 5 38106 Braunschweig Deutschland / Germany Tel: +49 (0)531 391-2634 Fax: +49 (0)531 391-7814 http://www.ift-bs.de -- 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] Box size for decoupled molecule in NpT ensemble
Dear Gromacs-users, I've a question regarding Gibbs free energy simulations. As the volume can fluctuate in the NpT-ensemble and is an extensive quantity, I do expect an intrinsic volume for the decoupled solute in the gas phase. Is there any chance to display this value? Regards, Andreas -- M. Sc. Andreas Mecklenfeld Stipendiat Technische Universität Braunschweig Institut für Thermodynamik Hans-Sommer-Straße 5 38106 Braunschweig Deutschland / Germany Tel: +49 (0)531 391-2634 Fax: +49 (0)531 391-7814 http://www.ift-bs.de -- 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] Error in comparison of Coulomb-14 potential?
Dear all, I want to perform an alchemical change of state of a molecule in TIP3P, where I do only change the partial charges of the atomtypes. To control my results, I perform two MD runs with the different charge sets respectively. I'm interested in the Coulomb-14 interactions of the solute (since TIP3P has none obviously) and would have expected that the potentials of the end states match those of the classic runs. For the classic MD, topology A results in -5.74e+02 kJ/mol, while for B it's -9.04e+02 kJ/mol which seems reasonable. However, the Coulomb-14 potential of alchemical state A (lambda = 0) is -5.74e+02 kJ/mol and for state B (lambda = 1) it's -5.69e+02 kJ/mol. I would have expected that the topology of the alchemical end state B matches topology B of the MD run, since all parameters should be the same. The results are the averages given in the log-files. Are my considerations wrong or could this be a bug in Gromacs? Thanks, Andreas -- M. Sc. Andreas Mecklenfeld Stipendiat Technische Universität Braunschweig Institut für Thermodynamik Hans-Sommer-Straße 5 38106 Braunschweig Deutschland / Germany Tel: +49 (0)531 391-2634 Fax: +49 (0)531 391-7814 http://www.ift-bs.de -- 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] gmx energy block averaging
Dear Gromacs-users, I've a question regarding the gmx energy functionality. I want to perform a block averaging with a prescribed number of data points in each block. The manual section of this command says "Note that in most cases the energy files contains averages over all MD steps, or over many more points than the number of frames in energy file." which is in accordance with the information given for the nstenergy-parameter "Note that the exact sums and fluctuations over all MD steps modulo nstcalcenergy are stored in the energy file, so g_energy can report exact energy averages and fluctuations also when nstenergy>1" I'm aware that I can give the number of blocks for the gmx energy evaluation with -nbmin respectively -nbmax, though I'm uncertain about the number of data points gmx energy actually uses for the block averaging. Say, I've performed 1e6 steps with nstenergy = 1000 and I want 5000 points per block - do I need 200 blocks in total? Thanks, Andreas -- M. Sc. Andreas Mecklenfeld Stipendiat Technische Universität Braunschweig Institut für Thermodynamik Hans-Sommer-Straße 5 38106 Braunschweig Deutschland / Germany Tel: +49 (0)531 391-2634 Fax: +49 (0)531 391-7814 http://www.ift-bs.de -- 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] Coulomb barriers and Coulomb Softcore Potential
Dear Mr. Shirts, thanks for your reply. My N/N_k ratio looks like this: Number of correlated and uncorrelated samples: StateN N_kN/N_k 0 613148319.06 1 613112219.28 2 613496117.16 3 61 937464.01 4 61 2249 266.86 5 61 532 1129.04 6 61 94 6384.18 7 61 485 1237.84 8 61 585 1027.03 9 61 1684 356.43 10 61 1047 573.48 11 61 820773.11 12 61 347 1731.24 13 61 2702 222.13 14 61 79 7692.14 15 61 193 3120.28 16 61 414 1451.40 17 615798510.35 18 6160589 9.90 19 6164621 9.28 With the following lambda distribution: ; init_lambda_state0 1 2 3 4 5 6 7 8 9 1011121314151617 18 19 vdw_lambdas = 0.000 0.224 0.378 0.489 0.578 0.657 0.730 0.802 0.881 0.976 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 coul_lambdas= 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.100 0.210 0.303 0.383 0.452 0.524 0.604 0.712 0.853 1.000 and lambda values 0 = decoupled / 1 = coupled. I use the LJ 1-1-6 SCP with alpha = 0.7 (I've checked alpha = 0.5 as well, but there is no significant difference), while Coulomb Softcore is not active. I've uploaded a diagram of Gibbs free energy difference over simulation time on github (https://github.com/AMecklenfeld/Ionic-Liquid/issues/1). The diagram contains some plateaus with high steps and slowly approaches a final value. From my point of view, it actually looks like my system is this slow. My idea was to use the Coulomb-SCP to flatten the energetic landscape. Another way would be expanded ensemble simulation, but since I use a constrained 4-site water model (triangle constraints), I've difficulties with shake in Gromacs 5.0.4. Do you have any suggestions? With kind regards, Andreas Mecklenfeld Am 24.08.2015 um 17:08 schrieb Michael Shirts: Adjusting the soft core is a gigantic pain. I wouldn't recommend it, and it's likely not necesssary. What settings are you using now? Note that the manual describes how it is defined. Can you post the alchemical-analysis output for N/N_k? There's an analysis quirk we are looking at where the correlation times are measured to be longer than they actually are, though that is when LJ is changing and coul is turned off. Look at the time correlation for the variable that is changing -- does it look stationary, or does it look like it's changing slowly, or has just a few discrete steps? If the autocorrelation time is slow, then N/N_k actually is that long, and the code is doing it's job. On Mon, Aug 24, 2015 at 9:55 AM, Andreas Mecklenfeld a.mecklenf...@tu-braunschweig.de wrote: Dear Gromacs-Users, I want to calculate the solvation free energy of water in an aqueous ionic solution and I'm using the Python tool alchemical-analysis.py by Klimovich, Shirts and Mobley for evaluation. This tool demonstrates a very high N/N_k ratio (up to 7000) while decreasing the electrostatic potential (Lennard Jones fully active). Considering energetic barriers, I would like to adjust the Coulomb Softcore Potential. Does this seem plausible and if so, how is the Coulomb Softcore Potential defined in Gromacs? Naden and Shirts provide a concept by equation (A.2) in Linear Basis Function Approach to Efficient Alchemical Free Energy Calculations. 2. Inserting and Deleting Particles with Coulombic Interactions (http://pubs.acs.org/doi/abs/10.1021/ct501047e) - is this the formula intended? Best regards, Andreas -- M. Sc. Andreas Mecklenfeld Stipendiat Technische Universität Braunschweig Institut für Thermodynamik Hans-Sommer-Straße 5 38106 Braunschweig Deutschland / Germany Tel: +49 (0)531 391-2634 Fax: +49 (0)531 391-7814 www.ift-bs.de -- 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. -- M. Sc. Andreas Mecklenfeld Stipendiat Technische Universität Braunschweig Institut für Thermodynamik Hans-Sommer-Straße 5 38106 Braunschweig Deutschland / Germany Tel: +49 (0)531 391-2634 Fax: +49 (0)531 391-7814 http://www.ift-bs.de -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support
[gmx-users] Coulomb barriers and Coulomb Softcore Potential
Dear Gromacs-Users, I want to calculate the solvation free energy of water in an aqueous ionic solution and I'm using the Python tool alchemical-analysis.py by Klimovich, Shirts and Mobley for evaluation. This tool demonstrates a very high N/N_k ratio (up to 7000) while decreasing the electrostatic potential (Lennard Jones fully active). Considering energetic barriers, I would like to adjust the Coulomb Softcore Potential. Does this seem plausible and if so, how is the Coulomb Softcore Potential defined in Gromacs? Naden and Shirts provide a concept by equation (A.2) in Linear Basis Function Approach to Efficient Alchemical Free Energy Calculations. 2. Inserting and Deleting Particles with Coulombic Interactions (http://pubs.acs.org/doi/abs/10.1021/ct501047e) - is this the formula intended? Best regards, Andreas -- M. Sc. Andreas Mecklenfeld Stipendiat Technische Universität Braunschweig Institut für Thermodynamik Hans-Sommer-Straße 5 38106 Braunschweig Deutschland / Germany Tel: +49 (0)531 391-2634 Fax: +49 (0)531 391-7814 www.ift-bs.de -- 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] Settle vs. 3 normal constraints
Dear Mark, thanks a lot for this advice - I've changed my .mdp to lincs-order = 8 and it works just fine! Andreas Am 30.07.2015 um 13:59 schrieb Mark Abraham: Hi, Using normal constraint algorithms with triangles of constraints can be tricky with some integrators. Do check out the several manual sections that talk about how these algorithms work, e.g. you may need to increase lincs-order Mark On Wed, Jul 29, 2015 at 5:47 PM Andreas Mecklenfeld a.mecklenf...@tu-braunschweig.de wrote: Dear GROMACS users, I want to calculate the solvation free energy of a rigid water molecule, e.g. TIP4P-Ew. To do this, I define one solute molecule which I refer to as couple-moltype in the .mdp-file (SOL). The solvens molecules are exactly the same, just named differently for distinction (SOLB). Since I can't simulate two molecule types with settle, I want to use constraints. My .itp-file looks like this: ; ; tip4pew Water model ; [ moleculetype ] ; molnamenrexcl SOL2 [ atoms ] ; id at type res nr res name at name cg nr chargemass 1 OW_tip4pew 1 SOL OW 1 0 16.0 2 HW_tip4pew 1 SOL HW1 1 0.52422 1.00800 3 HW_tip4pew 1 SOL HW2 1 0.52422 1.00800 4 MW1 SOL MW 1 -1.04844 0.0 [ constraints ] 1210.09572; func. 1: chemical bond (O-H) 1310.09572; func. 1: chemical bond (O-H) 2320.15139; func. 2: no chemical bond (H-H) [ virtual_sites3 ] ; Vsite from funct a b 4 1 2 3 1 0.106676721 0.106676721 [ exclusions ] 1234 2134 3124 4123 ; The position of the virtual site is computed as follows: ; ; O ; ; V ; ;HH ; ; Ewald tip4p: ; const = distance (OV) / [ cos (angle(VOH)) * distance (OH) ] ; 0.0125 nm/ [ cos (52.26 deg)* 0.09572 nm] ;then a = b = 0.5 * const = 0.106676721 ; ; Vsite pos x4 = x1 + a*(x2-x1) + b*(x3-x1) The temperature derivates by 20 K using the sd-intergrator as thermostat. By using the settle algorithm for only one molecule (same .mdp and .gro files as for the constrained), I gain results as expected. I'm sorry if this is a trivial question. Thanks for your support! Andreas -- M. Sc. Andreas Mecklenfeld Stipendiat Technische Universität Braunschweig Institut für Thermodynamik Hans-Sommer-Straße 5 38106 Braunschweig Deutschland / Germany Tel: +49 (0)531 391-2634 Fax: +49 (0)531 391-7814 http://www.ift-bs.de -- 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. -- M. Sc. Andreas Mecklenfeld Stipendiat Technische Universität Braunschweig Institut für Thermodynamik Hans-Sommer-Straße 5 38106 Braunschweig Deutschland / Germany Tel: +49 (0)531 391-2634 Fax: +49 (0)531 391-7814 http://www.ift-bs.de -- 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] Settle vs. 3 normal constraints
Dear GROMACS users, I want to calculate the solvation free energy of a rigid water molecule, e.g. TIP4P-Ew. To do this, I define one solute molecule which I refer to as couple-moltype in the .mdp-file (SOL). The solvens molecules are exactly the same, just named differently for distinction (SOLB). Since I can't simulate two molecule types with settle, I want to use constraints. My .itp-file looks like this: ; ; tip4pew Water model ; [ moleculetype ] ; molnamenrexcl SOL2 [ atoms ] ; id at type res nr res name at name cg nr chargemass 1 OW_tip4pew 1 SOL OW 1 0 16.0 2 HW_tip4pew 1 SOL HW1 1 0.52422 1.00800 3 HW_tip4pew 1 SOL HW2 1 0.52422 1.00800 4 MW1 SOL MW 1 -1.04844 0.0 [ constraints ] 1210.09572; func. 1: chemical bond (O-H) 1310.09572; func. 1: chemical bond (O-H) 2320.15139; func. 2: no chemical bond (H-H) [ virtual_sites3 ] ; Vsite from funct a b 4 1 2 3 1 0.106676721 0.106676721 [ exclusions ] 1234 2134 3124 4123 ; The position of the virtual site is computed as follows: ; ; O ; ; V ; ;HH ; ; Ewald tip4p: ; const = distance (OV) / [ cos (angle(VOH)) * distance (OH) ] ; 0.0125 nm/ [ cos (52.26 deg)* 0.09572 nm] ;then a = b = 0.5 * const = 0.106676721 ; ; Vsite pos x4 = x1 + a*(x2-x1) + b*(x3-x1) The temperature derivates by 20 K using the sd-intergrator as thermostat. By using the settle algorithm for only one molecule (same .mdp and .gro files as for the constrained), I gain results as expected. I'm sorry if this is a trivial question. Thanks for your support! Andreas -- M. Sc. Andreas Mecklenfeld Stipendiat Technische Universität Braunschweig Institut für Thermodynamik Hans-Sommer-Straße 5 38106 Braunschweig Deutschland / Germany Tel: +49 (0)531 391-2634 Fax: +49 (0)531 391-7814 http://www.ift-bs.de -- 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] Number of Compute Nodes in Gromacs Expanded Ensemble Simulations
Hi, I'm new to expanded ensemble simulations in Gromacs. Is there any rule of thumb for the most efficient number of compute nodes? Thanks in advance Andreas -- M. Sc. Andreas Mecklenfeld Stipendiat Technische Universität Braunschweig Institut für Thermodynamik Hans-Sommer-Straße 5 38106 Braunschweig Deutschland / Germany Tel: +49 (0)531 391-2634 Fax: +49 (0)531 391-7814 http://www.ift-bs.de -- 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.
