[gmx-users] Question on energygrps setting
Dear users, I know interaction energy calculation is carried out via energygrps setting in mdp file. Because free energy-related settings do not include this energygrps setting, so I think this energygrps setting may NOT be related to free energy settings. Could I ask whether my idea is correct or not? Thanks! Lei -- 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] Question on running gmx trjconv without 2 prompts
Thank you Dr. Lemkul, these two websites are very helpful. Thanks! On Thu, Apr 16, 2020 at 8:17 PM Justin Lemkul wrote: > > > On 4/16/20 8:12 PM, Lei Qian wrote: > > Dear users, > > > > Could I ask: how to run gmx trjconv without 2 prompts? > > I select 'Protein' to center, and 'System' to output. > > > > I put indexes of 'Protein' and 'System' into 1 .ndx file, add -n > > Protein_System.ndx to gmx trjconv command, however, Gromacs cannot do the > > selection automatically and asked me to choose from 'Protein' or > 'System'. > > http://manual.gromacs.org/documentation/5.1/onlinehelp/selections.html > http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts > > -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. > -- 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] Question on running gmx trjconv without 2 prompts
Dear users, Could I ask: how to run gmx trjconv without 2 prompts? I select 'Protein' to center, and 'System' to output. I put indexes of 'Protein' and 'System' into 1 .ndx file, add -n Protein_System.ndx to gmx trjconv command, however, Gromacs cannot do the selection automatically and asked me to choose from 'Protein' or 'System'. Thanks! Lei -- 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] question on dihedrals propers func 3 and impropers func 1
Dear users, Could I ask a question on dihedrals func types? Thanks! I used acpype to convert prmtop file and inpcrd file into gromacs files. However, in new generated top file, The dihedrals propers func is 3. and The dihedrals impropers func is 1. These two func types are different from propers func 9 and impropers func 4. (func type 9 and func type 4 can be found in Gromacs documents). Could I ask the meaning of func type 3 and func type 1 ? Thanks! Lei -- 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] question on system blow-up
Hi John,
Thank you very much for your reply.
After checking my log file, it seems my Metal ion cannot form a stable
coordination bonds in simulation.
the first 10 missing interactions, except for exclusions:
LJ-14 atoms 1180 1572 global 1180 1572
The number 1572 is my metal ion. And 1180 is an atom close to it in space.
Because it says "the first 10 missing interactions", but the file only
shows one missing interaction here LJ-14 atoms 1180 1572. It seems strange.
When I checked the trr file, the metal ion position shift away from its
normal position.
I will try to redo mcpb process.
On Fri, Sep 20, 2019 at 6:22 AM John Whittaker <
johnwhitt...@zedat.fu-berlin.de> wrote:
> Hi,
>
> > Dear gmx-users,
> >
> > Could I ask a question on system blow-up? Thanks!
> > I finished em, nvt, and npt. But when I ran production(npt) 10ns, I found
> > system blow up at around 1ns. ("atoms involved moved further apart than
> > the
> > multi-body cut-off distance")
> >
> > When I checked the trajectory files: nvt.trr, npt.trr, I found the
> > distorted water molecules (very very long H-O bond), although protein
> > looks
> > OK in these traj files. I guess perhaps those distorted water molecules
> > are
> > blow-up and they can gradually affect protein?
>
> It doesn't matter which molecule it is; if a molecule is blowing up, it
> will cause the simulation to fail. After visualizing your system, are you
> able to see what causes the elongated H-O bond? Are molecules overlapping?
> Are there other warnings (like LINCS warnings) in your output? You need to
> provide some more information about the system you are simulating or no
> one will really know how to help.
>
> >
> > I tried to change production npt setting to nvt (pcoupl = no), and change
> > integrator md to sd, change tau_t: 2.0 2.0. However, the following error
> > always show up:
> > "1 of the 20067 bonded interactions could not be calculated because some
> > atoms involved moved further apart than the multi-body cut-off distance
> > (1.18213 nm) or the two-body cut-off distance (1.241 nm)"
>
> These settings are likely not the cause of your problem and they probably
> wouldn't change much about the simulation consistently blowing up. When
> you make these changes, are the same molecules distorted?
>
> Best,
>
> John
>
> >
> > Thank you!
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
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> >
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> send
> > a mail to gmx-users-requ...@gromacs.org.
> >
>
>
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>
> * Please search the archive at
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> posting!
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[gmx-users] question on system blow-up
Dear gmx-users,
Could I ask a question on system blow-up? Thanks!
I finished em, nvt, and npt. But when I ran production(npt) 10ns, I found
system blow up at around 1ns. ("atoms involved moved further apart than the
multi-body cut-off distance")
When I checked the trajectory files: nvt.trr, npt.trr, I found the
distorted water molecules (very very long H-O bond), although protein looks
OK in these traj files. I guess perhaps those distorted water molecules are
blow-up and they can gradually affect protein?
I tried to change production npt setting to nvt (pcoupl = no), and change
integrator md to sd, change tau_t: 2.0 2.0. However, the following error
always show up:
"1 of the 20067 bonded interactions could not be calculated because some
atoms involved moved further apart than the multi-body cut-off distance
(1.18213 nm) or the two-body cut-off distance (1.241 nm)"
Thank you!
--
Gromacs Users mailing list
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http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
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Re: [gmx-users] Mutant_md_1ns.log, WT_md_1ns.log + 1 more item
Thanks Dr. Lemkul, This explanation makes sense to me. Thank you! Because I sent links to Both *gmx-us...@gromacs.org * and *gromacs.org_gmx-users@maillist.sys.kth.se * Please disregard the link I sent to *gromacs.org_gmx-users@maillist.sys.kth.se * Thank you again for your time and help! On Wed, Aug 28, 2019 at 11:05 AM Justin Lemkul wrote: > > > On 8/28/19 10:52 AM, Lei Qian (via Google Drive) wrote: > > I've shared some items with you: > > > > Mutant_md_1ns.log > > > https://drive.google.com/file/d/1qDoghj6Orc8yJTnLgvuhOERzMUfaH2Dd/view?usp=sharing=5d66951d > > > > > > WT_md_1ns.log > > > https://drive.google.com/file/d/1gSTOnEpIj6UcqnfuNS-TvOosQKJCWJsa/view?usp=sharing=5d66951d > > > > > > WT_md_10ns.log > > > https://drive.google.com/file/d/1UeLAcT4UZ6IpUKWJL7ahNRKmYmFt0Eeg/view?usp=sharing=5d66951d > > > > > > They're not attachments -- they're stored online. To open these items, > > just click the links above. > > > > Dear Users, > > > > Sorry for this inconvenience. > > Could I ask a question about Gromacs running time for my Wide Type and > > mutant protein (only 1 residue mutant)? Thanks! > > > > I attach the three log files here. > > (1) WT protein running for 1ns production step.(wall time: 1hour 40min). > > (2) WT protein running for 10ns production step (wall time: 6days 09h17). > > (3) Mutant protein running for 1ns production step. (wall time: > > 17hours 30min). > > > > From the log files, I can find each of them ran on one node with 24 > > cores. > > It seems the wall times for (1) and (2) do not have linearly > > proportional relationship. And (3) running took much longer time than > > I expected, since mutant protein is only one residue mutant. > > Was something else running when you did the 10-ns WT and 1-ns mutant > runs? Your 1-ns WT run is fast: > > (ns/day)(hour/ns) > Performance: 14.3481.673 > > But your 10-ns WT and 1-ns mutant are basically the same performance > (much slower): > > (WT) > (ns/day)(hour/ns) > Performance:1.566 15.329 > > (Mutant) > (ns/day)(hour/ns) > Performance:1.371 17.502 > > So I don't really see a difference between WT and mutant. The difference > in performance is likely due to the hardware or other processes being > run at the same time, causing a lag in performance. > > -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. -- 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] Mutant_md_1ns.log
I've shared an item with you: Mutant_md_1ns.log https://drive.google.com/file/d/1qDoghj6Orc8yJTnLgvuhOERzMUfaH2Dd/view?usp=sharing=5d66986b It's not an attachment -- it's stored online. To open this item, just click the link above. Dear Users, Sorry for this inconvenience. Could I ask a question about Gromacs wall-times for my Wide Type and mutant protein(only 1 residue mutant)? Thanks! I attach 3 log files here. (1) WT protein running for 1ns production step.(wall time: 1hour 40min). (2) WT protein running for 10ns production step (wall time: 6days 09h17). (3) Mutant protein running for 1ns production step. (wall time: 17hours 30min). From the log files, each ran on one node with 24 cores. It seems the wall times for (1) and (2) do not have linearly proportional relationship. And running time for (3) was much longer than I expected, since mutant protein is only 1 residue mutant protein. Thanks! -- 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] Mutant_md_1ns.log, WT_md_1ns.log + 1 more item
I've shared some items with you: Mutant_md_1ns.log https://drive.google.com/file/d/1qDoghj6Orc8yJTnLgvuhOERzMUfaH2Dd/view?usp=sharing=5d66951d WT_md_1ns.log https://drive.google.com/file/d/1gSTOnEpIj6UcqnfuNS-TvOosQKJCWJsa/view?usp=sharing=5d66951d WT_md_10ns.log https://drive.google.com/file/d/1UeLAcT4UZ6IpUKWJL7ahNRKmYmFt0Eeg/view?usp=sharing=5d66951d They're not attachments -- they're stored online. To open these items, just click the links above. Dear Users, Sorry for this inconvenience. Could I ask a question about Gromacs running time for my Wide Type and mutant protein (only 1 residue mutant)? Thanks! I attach the three log files here. (1) WT protein running for 1ns production step.(wall time: 1hour 40min). (2) WT protein running for 10ns production step (wall time: 6days 09h17). (3) Mutant protein running for 1ns production step. (wall time: 17hours 30min). From the log files, I can find each of them ran on one node with 24 cores. It seems the wall times for (1) and (2) do not have linearly proportional relationship. And (3) running took much longer time than I expected, since mutant protein is only one residue mutant. Thanks! -- 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] question on ffG43a1p force field
Hi Dr. Lemkul, Thank you for your reply. I have sent the links to you. Hope they could reach to you. The links include three log files. 1. WT protein running for 1ns production step.(wall time: 1h40min). 2. WT protein running for 10ns production step (wall time: 6d09h17). 3. Mutant protein running for 1ns production step. (wall time: 17h30min). >From the log, I can find each of them was run on one node with 24 cores. It seems the wall times for all these three files do not have linearly proportional relationship. Thanks for your time and help! Lei On Fri, Aug 23, 2019 at 3:42 PM Justin Lemkul wrote: > > > On 8/23/19 2:27 AM, Lei Qian wrote: > > Thank you Dr. Lemkul, > > I continued to use the GROMOS 43a1p for my simulation. > > > > I did simulation for 2 proteins separately: one is WT, the other one is > its > > one-residue mutant. > > And I finished em, NVT, NPT and 1 ns Production (4 steps) for both > proteins. > > > > However, I found for each of these 4 above steps, the wall time was a lot > > more longer for mutant than WT protein. > > Actually I used the same set of parameters for both proteins: e.g. same > mdp > > files for both protein in each step. > > Both proteins get acceptable results after 100-step NVT, 100-step NPT > etc., > > but the wall-time for mutant was much more longer than WT. > > Could I ask the reason for this? > > Sorry for this inconvenience. Thank you for your time and all your help! > > There is no way to know what is going on without seeing the .log files > from the runs and knowing the commands you gave. If you want to share > files, upload them to a file-sharing server and provide a link. The > mailing list does not accept attachments. > > -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. > -- 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] question on ffG43a1p force field
Thank you Dr. Lemkul, I continued to use the GROMOS 43a1p for my simulation. I did simulation for 2 proteins separately: one is WT, the other one is its one-residue mutant. And I finished em, NVT, NPT and 1 ns Production (4 steps) for both proteins. However, I found for each of these 4 above steps, the wall time was a lot more longer for mutant than WT protein. Actually I used the same set of parameters for both proteins: e.g. same mdp files for both protein in each step. Both proteins get acceptable results after 100-step NVT, 100-step NPT etc., but the wall-time for mutant was much more longer than WT. Could I ask the reason for this? Sorry for this inconvenience. Thank you for your time and all your help! Lei On Tue, Aug 20, 2019 at 8:23 AM Justin Lemkul wrote: > > > On 8/20/19 2:11 AM, Lei Qian wrote: > > Thank you Dr. Lemkul, > > Could I ask one more question? Thank you! > > > > When I did the step for adding ions and minimization and equilibration > > steps, one warning always showed up. > > So I had to add -maxwarn 2 after the command gmx grompp. > > This warning is as follows: > > > > WARNING 1 [file topol.top, line 48]: > >The GROMOS force fields have been parametrized with a physically > >incorrect multiple-time-stepping scheme for a twin-range cut-off. When > >used with a single-range cut-off (or a correct Trotter > >multiple-time-stepping scheme), physical properties, such as the > density, > >might differ from the intended values. Check if molecules in your > system > >are affected by such issues before proceeding. Further information > may be > >available at https://redmine.gromacs.org/issues/2884. > > > > It seems this warning is related to the GROMOS force field (for > > phosphorylation) you sent to me last week. > > Could I disregard this warning? > > There are significant concerns about the reproducibility of GROMOS force > fields. The authors of a recent study ( > https://pubs.acs.org/doi/10.1021/acs.jctc.8b00425) allege that GROMACS > has bugs that affect results, but the GROMACS developers maintain that > the GROMOS force fields were developed with incorrect algorithms in the > GROMOS software (hence the warning, and see the related Redmine issue > linked in the message). > > The issue is not specifically related to 43a1p (which is anyway an > extremely old force field), but all of the GROMOS parameter sets. > > Proceed with caution. There are other force field options available that > have been confirmed to work as expected across different software. > > -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. > -- 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] question on ffG43a1p force field
Thank you Dr. Lemkul, Could I ask one more question? Thank you! When I did the step for adding ions and minimization and equilibration steps, one warning always showed up. So I had to add -maxwarn 2 after the command gmx grompp. This warning is as follows: WARNING 1 [file topol.top, line 48]: The GROMOS force fields have been parametrized with a physically incorrect multiple-time-stepping scheme for a twin-range cut-off. When used with a single-range cut-off (or a correct Trotter multiple-time-stepping scheme), physical properties, such as the density, might differ from the intended values. Check if molecules in your system are affected by such issues before proceeding. Further information may be available at https://redmine.gromacs.org/issues/2884. It seems this warning is related to the GROMOS force field (for phosphorylation) you sent to me last week. Could I disregard this warning? Thanks! Lei On Sun, Aug 18, 2019 at 10:54 AM Justin Lemkul wrote: > > > On 8/18/19 3:24 AM, Lei Qian wrote: > > Could I ask one more question about your *gromos43a1p.ff* force filed ? > > Thanks! > > I ran $ gmx pdb2gmx -f myfile.pdb -o sort_processed.gro -water spce > > > > It shows a fatal error: > > "Fatal error: > > The residues in the chain xxx--xxx do not have a consistent type. The > first > > residue has type 'Protein', while residue *SEP is of type 'Other'*. > > Either there is a mistake in your chain, or it includes nonstandard > residue > > names that have not yet been added to the *residuetypes.dat file* in the > > GROMACS library directory." > > > > Then I found the *residuetypes.dat *in gromacs-2019.2/share/top, and add > > "SEP protein" to the list. > > However, the fatal error still shows up after this change. > > Could I ask how to solve this problem? > > You need to change the installed residuetypes.dat file, not the one in > the source. > > -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. > -- 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] question on ffG43a1p force field
Could I ask one more question about your *gromos43a1p.ff* force filed ? Thanks! I ran $ gmx pdb2gmx -f myfile.pdb -o sort_processed.gro -water spce It shows a fatal error: "Fatal error: The residues in the chain xxx--xxx do not have a consistent type. The first residue has type 'Protein', while residue *SEP is of type 'Other'*. Either there is a mistake in your chain, or it includes nonstandard residue names that have not yet been added to the *residuetypes.dat file* in the GROMACS library directory." Then I found the *residuetypes.dat *in gromacs-2019.2/share/top, and add "SEP protein" to the list. However, the fatal error still shows up after this change. Could I ask how to solve this problem? Thanks! On Fri, Aug 16, 2019 at 6:22 AM Justin Lemkul wrote: > > > On 8/16/19 2:15 AM, Lei Qian wrote: > > Sorry for this basic question. > > I read previous emails and tried to make pdb2gmx find ffG43a1p.ff. > > I added #include "ffG43a1p.itp" in FF.dat in ffG43a1p.ff folder. Also > tried > > to create a file called forcefield.doc and wrote "ffG43a1p" into it. > > I put these files in working directory > > and /usr/local/gromacs/share/gromacs/top/ directory. However, neither of > > them worked. > > Could I ask how to solve this problem? > > It sounds like you are trying to modify a very old and outdated version > of the files (potentially with an outdated version of GROMACS - FF.dat > is no longer used). The files you want for any post-4.0 version of > GROMACS are in: > > http://www.gromacs.org/@api/deki/files/235/=gromos43a1p-4.5.1.tgz > > -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. > -- 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] question on ffG43a1p force field
Thank you very much Dr. Lemkul, I downloaded your file and it works! Actually I downloaded the previous file from Gromacs web: http://www.gromacs.org/Downloads/User_contributions/Force_fields Thanks again for your help! On Fri, Aug 16, 2019 at 6:22 AM Justin Lemkul wrote: > > > On 8/16/19 2:15 AM, Lei Qian wrote: > > Sorry for this basic question. > > I read previous emails and tried to make pdb2gmx find ffG43a1p.ff. > > I added #include "ffG43a1p.itp" in FF.dat in ffG43a1p.ff folder. Also > tried > > to create a file called forcefield.doc and wrote "ffG43a1p" into it. > > I put these files in working directory > > and /usr/local/gromacs/share/gromacs/top/ directory. However, neither of > > them worked. > > Could I ask how to solve this problem? > > It sounds like you are trying to modify a very old and outdated version > of the files (potentially with an outdated version of GROMACS - FF.dat > is no longer used). The files you want for any post-4.0 version of > GROMACS are in: > > http://www.gromacs.org/@api/deki/files/235/=gromos43a1p-4.5.1.tgz > > -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. > -- 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] question on ffG43a1p force field
Sorry for this basic question. I read previous emails and tried to make pdb2gmx find ffG43a1p.ff. I added #include "ffG43a1p.itp" in FF.dat in ffG43a1p.ff folder. Also tried to create a file called forcefield.doc and wrote "ffG43a1p" into it. I put these files in working directory and /usr/local/gromacs/share/gromacs/top/ directory. However, neither of them worked. Could I ask how to solve this problem? Thanks lei -- 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.
