[gmx-users] Water model choice
Hi all, Which water model is best to use with the CHARMM27 FF, Tip3p or SPC/E? I know the CHARMM FF has been optimised with Tip3p, but I also know that SPC/E water model has good agreement with experimental data e.g. diffusion coefficient. Any guidance will be much appreciated? Akash -- 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] Water model choice
On 6/17/19 6:58 AM, Pandya, Akash wrote: Hi all, Which water model is best to use with the CHARMM27 FF, Tip3p or SPC/E? I know the CHARMM FF has been optimised with Tip3p, but I also know that SPC/E water model has good agreement with experimental data e.g. diffusion coefficient. Any guidance will be much appreciated? Use the CHARMM-modified TIP3P. You can't look at a water model's performance in isolation and just change it. Every force field was designed for use with a given water model. There are some instances in which this is flexible (e.g. certain water model properties compensating for inadequacies in AMBER LJ parameters) but this is not a generally applicable practice. If you change the water model, you risk completely changing charge screening, therefore subjecting your simulation to unpredictable electrostatic artifacts. Also use CHARMM36 rather than the outdated "CHARMM27" force field. It is better in every respect for proteins, lipids, nucleic acids, etc. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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] water model in use of UFF
Dear Justin,Given that I'm using UFF for all atoms in MOF,Is it true that I build a water molecule from "http://software-lisc.fbk.eu/obgmx/index.php"; site and include it on my topol.top? Thanks,Ganj -- 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] Citrate topology in Charmm36 FF
Hi all, I'm simulating Citrate in water using the Charmm36 FF. I get this error in my topology. I have used the same topology for charmm27 ff and had no problems. ERROR 1 [file CITMolecule.itp, line 63]: No default Bond types ERROR 2 [file CITMolecule.itp, line 64]: No default Bond types ERROR 3 [file CITMolecule.itp, line 71]: No default Bond types ERROR 4 [file CITMolecule.itp, line 72]: No default Bond types ERROR 5 [file CITMolecule.itp, line 81]: No default U-B types ERROR 6 [file CITMolecule.itp, line 82]: No default U-B types ERROR 7 [file CITMolecule.itp, line 84]: No default U-B types ERROR 8 [file CITMolecule.itp, line 97]: No default U-B types ERROR 9 [file CITMolecule.itp, line 98]: No default U-B types ERROR 10 [file CITMolecule.itp, line 100]: No default U-B types My topology file is pasted here with the relevant parts: [ bondtypes ] CC OC 1 0.126 439320.0 OH1H 1 0.096 456056.0 CT CC 1 0.152 167360.0 CT2CT 1 0.150 186188.0 CT OH1 1 0.142 358150.4 [ angletypes ] OCCCOC 5 124.00 836.80 0.2225 58576.000 OCCC CT2 5 118.00 334.72 0.2388 41840.000 CTCCOC 5 118.00 334.72 0.2388 41840.000 CT2 CTCC 5 108.00 435.14 0. 0.000 CT2 CT CT2 5 113.60 488.27 0.25619338.688 HA CT2CT 5 110.10 279.74 0.2179 18853.104 CC CT2CT 5 108.00 435.14 0. 0.000 CT2 CT OH1 5 110.10 633.46 0. 0.000 OH1 CTCC 5 110.10 633.46 0. 0.000 CT OH1 H 5 106.00 481.16 0. 0.000 [ dihedraltypes ] HA CT2CC OC 9 180.00 0.2092 6 CT CT2CC OC 9 180.00 0.2092 6 CT2 CT CT2 CC 9 0.00 4. 3 OH1 CT CT2 CC 9 0.00 0.8368 3 OH1 CT CT2 HA 9 0.00 0.8368 3 CCCT CT2 CC 9 0.00 0.8368 3 CCCT CT2 HA 9 0.00 0.8368 3 CT2 CT CT2 HA 9 0.00 0.8368 3 OH1 CTCC OC 9 0.00 1.2000 2 CT2 CTCC OC 9 180.00 0.2092 6 CCCT OH1H 9 0.00 0.2092 1 CT2 CT OH1H 9 0.00 0.5858 3 CC CT2OC OC 2 0.00 803.328 CCCTOC OC 2 0.00 803.328 [ moleculetype ] CIT 3 [ atoms ] 1 CC 1 CIT C 1 0.62012.011 2 CT2 1 CIT C 2 -0.18012.011 3 CT 1 CIT C 3 -0.07012.011 4 CC 1 CIT C 4 0.62012.011 5 CT2 1 CIT C 5 -0.18012.011 6 CC 1 CIT C 6 0.62012.011 7 OC 1 CIT O 7 -0.76015.999 8 OC 1 CIT O 8 -0.76015.999 9 OC 1 CIT O 9 -0.76015.999 10 OC 1 CIT O 10 -0.76015.999 11 OC 1 CIT O 11 -0.76015.999 12 OC 1 CIT O 12 -0.76015.999 13 OH1 1 CIT O 13 -0.54015.999 14 HA 1 CIT H 14 0.090 1.008 15 HA 1 CIT H 15 0.090 1.008 16 HA 1 CIT H 16 0.090 1.008 17 HA 1 CIT H 17 0.090 1.008 18 H1 CIT H 18 0.310 1.008 [ bonds ] 1 81 1 71 1 2 1 2 15 1 2 14 1 2 31 3 13 1 3 51 3 41 4 10 1 4 91 5 17 1 5 16 1 5 61 6 12 1 6 11 1 13 18 1 [ angles ] 8 1 7 5 8 1 2 5 7 1 2 5 1 215 5 15214 5 152 3 5 1 214 5 142 3 5 1 2 3 5 2 313 5 133 5 5 133 4 5 2 3 5 5 5 3 4 5 2 3 4 5 3 410 5 104 9 5 3 4 9 5 3 517 5 17516 5 175 6 5 3 516 5 165 6 5 3 5 6 5 5 612 5 12611 5 5 611 5 31318 5 [ exclusions ] 18 9 10 [ pairs ] 10 18 2 0.3 -0.760 0.310 0.17145 0.310857 9 18 2 0.3 -0.760 0.310 0.17145 0.310857 [ dihedrals ] 812 15 9 712 15 9 812 14 9 712 14 9 8123 9 7123 9 123 13 9 15 23 13 9 14 23 13 9 1235 9 15 235 9 14 235 9 1234 9 15 234 9 14 234 9 23 13 18 9 53 13 18 9 43 13 18 9 235 17 9 13 35 17 9 435 17 9 235 16 9 13 35 16 9 435 16 9 2356 9 13 356 9 4356 9 234 10 9 13 34 10 9 534 10 9 2349 9 13 349 9 5349 9 356 12 9 17 56 12 9 16 56 12 9 356 11 9 17 56 11 9 16 56 11 9 [ dihedrals ] 1 2 7 8 2 4 3 9 102 6 5 11122 #ifdef POSRES_CITMolecule [ position_restraints ] ; atom type fx fy fz 1 1 1000 1000 1000 2 1 1000 1000 1000 3 1 1000 1000 1000 4 1 1000 1000 1000 5 1 1000 1000 1000 6 1 1000 1000 1000 7 1 1000 1000 1000 8 1 1000 1000 1000 9 1 1000 1000 1000 10 1 1000 1000 1000 1
[gmx-users] Error in MD simulation
Dear GMX Users, in Gromacs 18.1, May you please kindly help me with this error: Cannot run short-ranged nonbonded interactions on a GPU because there is none detected. after doing this command: gmx mdrun -deffnm md_0_1 -nb gpu Many thanks. +Mahmoud -- 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] correcting timesteps
Hello I fudged a restart on gromacs 2018 and am missing 195 femtoseconds from my trajectory. This shouldn't matter because I only need a 10 picosecond resolution trajectory. However, when I try to correct the timestep with trjconv and -timestep it doesnt seem to have done anything. *gmx trjconv -f 40t84_10p_concat.xtc -timestep 10 -o 40t84_10p_concat_10.xtc* This command worked but when running *gmx check* on the new trajectory afterward there are still a bunch of timesteps don't match errors. gmx check -f 40t84_10p_concat_10.xtc ^MReading frame 0 time 4000.000 # Atoms 1716 Precision 0.001 (nm) ^MReading frame 1 time 4008.000 ^MReading frame 2 time 4020.000 Timesteps at t=4e+07 don't match (8, 12) ^MReading frame 3 time 4032.000 ^MReading frame 4 time 4040.000 Timesteps at t=4e+07 don't match (12, 8) ^MReading frame 5 time 4048.000 ^MReading frame 6 time 4060.000 -- 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] Error in MD simulation
Hi, That means what it says - GROMACS couldn't detect a GPU. Generally that means the driver is unhappy, etc. perhaps after a software update. Try a reboot or a reinstall of the CUDA package. Mark On Mon, 17 Jun 2019 at 16:14, Mahmoud Mirzaei wrote: > Dear GMX Users, > > in Gromacs 18.1, May you please kindly help me with this error: > > Cannot run short-ranged nonbonded interactions on a GPU because there is > none detected. > after doing this command: > gmx mdrun -deffnm md_0_1 -nb gpu > > Many thanks. > +Mahmoud > -- > 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] Grompp not producing tpr files
Thanks again for the replies, I'm currently using gromacs 2019.3, and I'm creating a simple system with only a monomer in water. The monomer's topology was created using TPP, for use with the OPLS force field. After adding the new residue to the force field, I'm able to run "pdb2gmx", "editconf", and "solvate" with no issues to create the system. It's when I try to "grompp" that the segmentation fault occurs. The only thing that stands out is the system's charge. After running pdb2gmx, the system's overall charge is listed as -1.589 e. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Paul Bauer Sent: Thursday, June 13, 2019 8:08:58 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Grompp not producing tpr files Hello, Yes, the last part indicates an error that should not happen. Which version did you use to run this? If it is a version before 2018, can you try the newer versions to see if the error persists? Cheers Paul On Thu, 13 Jun 2019, 17:04 Israel Estrada, wrote: > Thanks for the replies! > > Mark, the process seemed to "finish" properly (my terminal did not close, > and the command line was waiting for the next command as if it ran > normally). I looked for the output file (ions.tpr) in the working > directory, or any new files, but nothing was generated. > > Bratin, here is what my terminal displayed, > "command line: > gmx grompp -f ions.mdp -c box.gro -o ions.tpr -p topol.top > > Setting the LD random seed to 973096069 > Segmentation fault (core dumped)" > The last part seems to be the error, right? > > Thanks again!! > -Israel > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Bratin > Kumar Das <177cy500.bra...@nitk.edu.in> > Sent: Wednesday, June 12, 2019 7:00:55 PM > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Grompp not producing tpr files > > Hi >Give here the full error > > On Thu 13 Jun, 2019, 1:35 AM Mark Abraham, > wrote: > > > Hi, > > > > Was grompp exiting normally, or crashing? Are you looking in the right > > place, for a file of the right name? :-) > > > > Mark > > > > On Wed., 12 Jun. 2019, 18:42 Israel Estrada, wrote: > > > > > Hello users, > > > > > > > > > I'm running into problems trying to grompp; I'm using the command > > > > > > > > > gmx grompp -f ions.mdp -c etc_box.gro -o ions.tpr -p topol.top > > > > > > > > > and the process shows no error messages, but output files are not being > > > generated. I'm running this on a small molecule, about 20 atoms, with > the > > > hopes that I can modify OPLS parameters as needed. I'm sure the problem > > is > > > related to an error in the topology files, but I don't know how or if I > > can > > > fix this. > > > > > > > > > Any help would be greatly appreciated, thank you! > > > > > > -Israel > > > -- > > > 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 > https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists%2FGMX-Users_List&data=02%7C01%7Cisraele%40cpp.edu%7C47478c78e1374be2cfc808d6f0111ee0%7C164ba61e39ec4f5d89ffaa1f00a521b4%7C0%7C0%7C636960353657481277&sdata=Dhpf8PmGt%2FGXEMzr1hRsXPmvYwPC3VUbJyyD2Bw%2BLf8%3D&reserved=0 > before > posting! > > * Can't post? Read > https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists&data=02%7C01%7Cisraele%40cpp.edu%7C47478c78e1374be2cfc808d6f0111ee0%7C164ba61e39ec4f5d89ffaa1f00a521b4%7C0%7C0%7C636960353657481277&sdata=ZoSDYsTKHtbWZx%2FcgFJ%2FEqg7yeGhY8ULTBzey9CKvx0%3D&reserved=0 > > * For (un)subscribe requests visit > https://nam03.safelinks.protection.outlook.com/
Re: [gmx-users] Grompp not producing tpr files
Before you go any further you need to correct the topology. The complete molecule should only have an integer charge, and if it does have a charge then neutralise the system with counter ions. http://www.gromacs.org/Documentation/Errors#System_has_non-zero_total_charge On Tue, 18 Jun. 2019, 1:17 pm Israel Estrada, wrote: > Thanks again for the replies, > > > I'm currently using gromacs 2019.3, and I'm creating a simple system with > only a monomer in water. The monomer's topology was created using TPP, for > use with the OPLS force field. > > > After adding the new residue to the force field, I'm able to run > "pdb2gmx", "editconf", and "solvate" with no issues to create the system. > It's when I try to "grompp" that the segmentation fault occurs. > > > The only thing that stands out is the system's charge. After running > pdb2gmx, the system's overall charge is listed as -1.589 e. > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Paul > Bauer > Sent: Thursday, June 13, 2019 8:08:58 AM > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Grompp not producing tpr files > > Hello, > > Yes, the last part indicates an error that should not happen. > > Which version did you use to run this? > > If it is a version before 2018, can you try the newer versions to see if > the error persists? > > Cheers > > Paul > > > > On Thu, 13 Jun 2019, 17:04 Israel Estrada, wrote: > > > Thanks for the replies! > > > > Mark, the process seemed to "finish" properly (my terminal did not close, > > and the command line was waiting for the next command as if it ran > > normally). I looked for the output file (ions.tpr) in the working > > directory, or any new files, but nothing was generated. > > > > Bratin, here is what my terminal displayed, > > "command line: > > gmx grompp -f ions.mdp -c box.gro -o ions.tpr -p topol.top > > > > Setting the LD random seed to 973096069 > > Segmentation fault (core dumped)" > > The last part seems to be the error, right? > > > > Thanks again!! > > -Israel > > > > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Bratin > > Kumar Das <177cy500.bra...@nitk.edu.in> > > Sent: Wednesday, June 12, 2019 7:00:55 PM > > To: gmx-us...@gromacs.org > > Subject: Re: [gmx-users] Grompp not producing tpr files > > > > Hi > >Give here the full error > > > > On Thu 13 Jun, 2019, 1:35 AM Mark Abraham, > > wrote: > > > > > Hi, > > > > > > Was grompp exiting normally, or crashing? Are you looking in the right > > > place, for a file of the right name? :-) > > > > > > Mark > > > > > > On Wed., 12 Jun. 2019, 18:42 Israel Estrada, wrote: > > > > > > > Hello users, > > > > > > > > > > > > I'm running into problems trying to grompp; I'm using the command > > > > > > > > > > > > gmx grompp -f ions.mdp -c etc_box.gro -o ions.tpr -p topol.top > > > > > > > > > > > > and the process shows no error messages, but output files are not > being > > > > generated. I'm running this on a small molecule, about 20 atoms, with > > the > > > > hopes that I can modify OPLS parameters as needed. I'm sure the > problem > > > is > > > > related to an error in the topology files, but I don't know how or > if I > > > can > > > > fix this. > > > > > > > > > > > > Any help would be greatly appreciated, thank you! > > > > > > > > -Israel > > > > -- > > > > 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 > > > https://nam03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSu
