Re: [gmx-users] question on ffG43a1p force field
On 8/27/19 11:17 AM, Lei Qian wrote: 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. Please share the .log files with the list, not just with me. -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.
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
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.
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
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.
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
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.
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.
Re: [gmx-users] question on ffG43a1p force field
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.
[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.
