Re: [gmx-users] Doubt about Free Energy control Minimization
On 7/6/17 8:42 AM, Varvdekar Bhagyesh Rajendra wrote: Dear Justin, It would be helpful if you please explain in a bit more detail about the impact of the settings of table-extension. The manual says "Extension of the non-bonded potential lookup tables beyond the largest cut-off distance", but a better insight from you would be definitely more very useful. I have a slightest idea that it is useful to save computational time. It that is considered true, it shouldn't affect the results, should it? I would appreciate if you could explain how increasing table-extension can cause permit distorted structures. I performed a short study of the effect on increasing table-extension from 1 nm to 10 nm onwards in increments of 1 nm. The inter and intra molecular energies increased from 1 nm to 4 nm and then were almost the same and with the minimization without any free energy code. Hence, I suspect that table-extension with 4 nm onwards takes into account all interactions while the free energy change goes on. I would appreciate if you could offer any comment on my deduction. If you increase the table-lookup length, you tell mdrun that it is OK to find things like 1-4 interactions at some very long distance. Normally when a 1-4 goes beyond 1 nm, it is a sign of trouble. If you make it normal, you turn a blind eye to possible problems. I couldn't find any distorted structures while the study though, could you suggest any criteria so as to consider if any structure has evolved into a distorted one? Is there any other way where I can avoid the said warning other than increasing table-extension and maintaining couple-intramol = no in my minimizing code with the free energy addendum. No idea, sorry. And unfortunately it appears that no one else on the mailing list has any idea about what's going on in your system, either. Maybe someone else will chip in... -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Doubt about Free Energy control Minimization
Dear Justin, It would be helpful if you please explain in a bit more detail about the impact of the settings of table-extension. The manual says "Extension of the non-bonded potential lookup tables beyond the largest cut-off distance", but a better insight from you would be definitely more very useful. I have a slightest idea that it is useful to save computational time. It that is considered true, it shouldn't affect the results, should it? I would appreciate if you could explain how increasing table-extension can cause permit distorted structures. I performed a short study of the effect on increasing table-extension from 1 nm to 10 nm onwards in increments of 1 nm. The inter and intra molecular energies increased from 1 nm to 4 nm and then were almost the same and with the minimization without any free energy code. Hence, I suspect that table-extension with 4 nm onwards takes into account all interactions while the free energy change goes on. I would appreciate if you could offer any comment on my deduction. I couldn't find any distorted structures while the study though, could you suggest any criteria so as to consider if any structure has evolved into a distorted one? Is there any other way where I can avoid the said warning other than increasing table-extension and maintaining couple-intramol = no in my minimizing code with the free energy addendum. Thank you, Bhagyesh - Original Message - From: "Varvdekar Bhagyesh Rajendra" To: gmx-us...@gromacs.org Sent: Friday, June 30, 2017 2:24:09 AM Subject: Re: [gmx-users] Doubt about Free Energy control Minimization Dear Justin, It would be helpful if you please explain in a bit more detail about the impact of the settings of table-extension. The manual says "Extension of the non-bonded potential lookup tables beyond the largest cut-off distance", but a better insight from you would be definitely more very useful. I have a slightest idea that it is useful to save computational time. It that is considered true, it shouldn't affect the results, should it? I would appreciate if you could explain how increasing table-extension can cause permit distorted structures. Is there any other way where I can avoid the said warning other than increasing table-extension and maintaining couple-intramol = no in my minimizing code with the free energy addendum. Thank you, Bhagyesh - Original Message - From: "Justin Lemkul" To: gmx-us...@gromacs.org Sent: Thursday, June 29, 2017 6:48:25 PM Subject: Re: [gmx-users] Doubt about Free Energy control Minimization On 6/29/17 5:11 AM, Varvdekar Bhagyesh Rajendra wrote: > Dear Justin, > > I am getting the same following warning even after minimizing the system > twice using cg integrator. This is only when the free energy stuff is > inserted in the energy minimization code. > > " WARNING: Listed nonbonded interaction between particles 2263 and 2298 at > distance 3f which is larger than the table limit 3f nm. > > This is likely either a 1,4 interaction, or a listed interaction inside a > smaller molecule you are decoupling during a free energy calculation. Since > interactions at distances beyond the table cannot be computed, they are > skipped until they are inside the table limit again. You will only see this > message once, even if it occurs for several interactions. > > IMPORTANT: This should not happen in a stable simulation, so there is > probably something wrong with your system. Only change the table-extension > distance in the mdp file if you are really sure that is the reason. " > > > When the system is minimized without free energy code, it shows no warning. > Hence, I suppose it is due to the free energy code itself with > couple-intramol = no. > > I found the warning disappears when couple-intramol = yes. But this is not I > would like to do, since intra molecular interactions need not be > scaled/perturbed. > > It's definitely true that the "listed interaction inside a smaller molecule > you are decoupling during a free energy calculation". > > When the table-extension is increased to 4 nm with couple-intramol = no, the > warning again disappears. Should I go forward with this setting and how will > it affect the energy minimization of my system? > Increasing the table-extension means mdrun will permit distorted structures that may be totally unreasonable. It is generally unwise to increase it, and especially if you're increasing it that much. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem
Re: [gmx-users] Doubt about Free Energy control Minimization
Dear Justin, It would be helpful if you please explain in a bit more detail about the impact of the settings of table-extension. The manual says "Extension of the non-bonded potential lookup tables beyond the largest cut-off distance", but a better insight from you would be definitely more very useful. I have a slightest idea that it is useful to save computational time. It that is considered true, it shouldn't affect the results, should it? I would appreciate if you could explain how increasing table-extension can cause permit distorted structures. Is there any other way where I can avoid the said warning other than increasing table-extension and maintaining couple-intramol = no in my minimizing code with the free energy addendum. Thank you, Bhagyesh - Original Message - From: "Justin Lemkul" To: gmx-us...@gromacs.org Sent: Thursday, June 29, 2017 6:48:25 PM Subject: Re: [gmx-users] Doubt about Free Energy control Minimization On 6/29/17 5:11 AM, Varvdekar Bhagyesh Rajendra wrote: > Dear Justin, > > I am getting the same following warning even after minimizing the system > twice using cg integrator. This is only when the free energy stuff is > inserted in the energy minimization code. > > " WARNING: Listed nonbonded interaction between particles 2263 and 2298 at > distance 3f which is larger than the table limit 3f nm. > > This is likely either a 1,4 interaction, or a listed interaction inside a > smaller molecule you are decoupling during a free energy calculation. Since > interactions at distances beyond the table cannot be computed, they are > skipped until they are inside the table limit again. You will only see this > message once, even if it occurs for several interactions. > > IMPORTANT: This should not happen in a stable simulation, so there is > probably something wrong with your system. Only change the table-extension > distance in the mdp file if you are really sure that is the reason. " > > > When the system is minimized without free energy code, it shows no warning. > Hence, I suppose it is due to the free energy code itself with > couple-intramol = no. > > I found the warning disappears when couple-intramol = yes. But this is not I > would like to do, since intra molecular interactions need not be > scaled/perturbed. > > It's definitely true that the "listed interaction inside a smaller molecule > you are decoupling during a free energy calculation". > > When the table-extension is increased to 4 nm with couple-intramol = no, the > warning again disappears. Should I go forward with this setting and how will > it affect the energy minimization of my system? > Increasing the table-extension means mdrun will permit distorted structures that may be totally unreasonable. It is generally unwise to increase it, and especially if you're increasing it that much. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Doubt about Free Energy control Minimization
On 6/29/17 5:11 AM, Varvdekar Bhagyesh Rajendra wrote: Dear Justin, I am getting the same following warning even after minimizing the system twice using cg integrator. This is only when the free energy stuff is inserted in the energy minimization code. " WARNING: Listed nonbonded interaction between particles 2263 and 2298 at distance 3f which is larger than the table limit 3f nm. This is likely either a 1,4 interaction, or a listed interaction inside a smaller molecule you are decoupling during a free energy calculation. Since interactions at distances beyond the table cannot be computed, they are skipped until they are inside the table limit again. You will only see this message once, even if it occurs for several interactions. IMPORTANT: This should not happen in a stable simulation, so there is probably something wrong with your system. Only change the table-extension distance in the mdp file if you are really sure that is the reason. " When the system is minimized without free energy code, it shows no warning. Hence, I suppose it is due to the free energy code itself with couple-intramol = no. I found the warning disappears when couple-intramol = yes. But this is not I would like to do, since intra molecular interactions need not be scaled/perturbed. It's definitely true that the "listed interaction inside a smaller molecule you are decoupling during a free energy calculation". When the table-extension is increased to 4 nm with couple-intramol = no, the warning again disappears. Should I go forward with this setting and how will it affect the energy minimization of my system? Increasing the table-extension means mdrun will permit distorted structures that may be totally unreasonable. It is generally unwise to increase it, and especially if you're increasing it that much. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Doubt about Free Energy control Minimization
Dear Justin, I am getting the same following warning even after minimizing the system twice using cg integrator. This is only when the free energy stuff is inserted in the energy minimization code. " WARNING: Listed nonbonded interaction between particles 2263 and 2298 at distance 3f which is larger than the table limit 3f nm. This is likely either a 1,4 interaction, or a listed interaction inside a smaller molecule you are decoupling during a free energy calculation. Since interactions at distances beyond the table cannot be computed, they are skipped until they are inside the table limit again. You will only see this message once, even if it occurs for several interactions. IMPORTANT: This should not happen in a stable simulation, so there is probably something wrong with your system. Only change the table-extension distance in the mdp file if you are really sure that is the reason. " When the system is minimized without free energy code, it shows no warning. Hence, I suppose it is due to the free energy code itself with couple-intramol = no. I found the warning disappears when couple-intramol = yes. But this is not I would like to do, since intra molecular interactions need not be scaled/perturbed. It's definitely true that the "listed interaction inside a smaller molecule you are decoupling during a free energy calculation". When the table-extension is increased to 4 nm with couple-intramol = no, the warning again disappears. Should I go forward with this setting and how will it affect the energy minimization of my system? Best Regards, Bhagyesh - Original Message - From: "Justin Lemkul" To: gmx-us...@gromacs.org Sent: Wednesday, June 28, 2017 7:17:34 AM Subject: Re: [gmx-users] Doubt about Free Energy control Minimization On 6/27/17 7:43 AM, Varvdekar Bhagyesh Rajendra wrote: > Dear Justin, > > When the system is minimized with full interactions with no free energy code, > I see no warnings and the systems is minimized properly. > > However, when the free energy code is added with couple-intramol = no, I > encounter the said warning, but still the system can be minimized ignoring > the warning. > > When the free energy code is added with couple-intramol = yes, there's no > warning, but the system is again well minimized. > You may need several rounds of energy minimization to get a stable result. Your final minimization and equilibration should be done under the conditions/settings that make the most sense for you to model. -Justin > I would like to learn if its reasonable to ignore the warning in the case > where couple-intramol = no, since I am dealing with a peptide and > intramolecular interactions can suppress the intermolecular interactions. > > I intend to perform normal-mode calculations on the resulting intermediates > which are divergent from the Binding energy simulations requiring > convergence. Hence, I presume there shouldn't be much complication in this > case. I understand the approach seems quite outlandish, but still I aspire to > execute the same. Any opinions and/or suggestions in this procedure will be > greatly helpful. > > Many thanks, > > Bhagyesh. > > > - Original Message ----- > From: "Justin Lemkul" > To: gmx-us...@gromacs.org > Sent: Tuesday, June 27, 2017 6:42:33 PM > Subject: Re: [gmx-users] Doubt about Free Energy control Minimization > > On 6/26/17 9:09 AM, Varvdekar Bhagyesh Rajendra wrote: >> Dear Justin, >> >> I have encountered the following warning when I used the following code to >> minimize my protein-ligand system when the interaction potential energy >> between the protein and the ligand are multiplied by 0.9, 0.8, 0.7,..., 0.2, >> 0.1. >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/Files/em_steep.mdp >> >> Warning: 1-4 interaction between 2263 and 2298 at distance 1.004 which is >> larger than the 1-4 table size 1.000 nm >> These are ignored for the rest of the simulation >> This usually means your system is exploding, >> if not, you should increase table-extension in your mdp file >> or with user tables increase the table size >> >> >> I suppose this error is due to setting couple-intramol = no. When it is set >> to yes, the warning vanishes. >> >> But, this is my desired setting since, I do not intend to scale the intra >> molecular interactions even though the ligand is a peptide. Is it reasonable >> to ignore the warning. If not , how can it affect my resulting structure ? >> And are all such interaction "ignored for the rest of the simulation" ? >> > &g
Re: [gmx-users] Doubt about Free Energy control Minimization
On 6/27/17 7:43 AM, Varvdekar Bhagyesh Rajendra wrote: Dear Justin, When the system is minimized with full interactions with no free energy code, I see no warnings and the systems is minimized properly. However, when the free energy code is added with couple-intramol = no, I encounter the said warning, but still the system can be minimized ignoring the warning. When the free energy code is added with couple-intramol = yes, there's no warning, but the system is again well minimized. You may need several rounds of energy minimization to get a stable result. Your final minimization and equilibration should be done under the conditions/settings that make the most sense for you to model. -Justin I would like to learn if its reasonable to ignore the warning in the case where couple-intramol = no, since I am dealing with a peptide and intramolecular interactions can suppress the intermolecular interactions. I intend to perform normal-mode calculations on the resulting intermediates which are divergent from the Binding energy simulations requiring convergence. Hence, I presume there shouldn't be much complication in this case. I understand the approach seems quite outlandish, but still I aspire to execute the same. Any opinions and/or suggestions in this procedure will be greatly helpful. Many thanks, Bhagyesh. - Original Message - From: "Justin Lemkul" To: gmx-us...@gromacs.org Sent: Tuesday, June 27, 2017 6:42:33 PM Subject: Re: [gmx-users] Doubt about Free Energy control Minimization On 6/26/17 9:09 AM, Varvdekar Bhagyesh Rajendra wrote: Dear Justin, I have encountered the following warning when I used the following code to minimize my protein-ligand system when the interaction potential energy between the protein and the ligand are multiplied by 0.9, 0.8, 0.7,..., 0.2, 0.1. http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/Files/em_steep.mdp Warning: 1-4 interaction between 2263 and 2298 at distance 1.004 which is larger than the 1-4 table size 1.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size I suppose this error is due to setting couple-intramol = no. When it is set to yes, the warning vanishes. But, this is my desired setting since, I do not intend to scale the intra molecular interactions even though the ligand is a peptide. Is it reasonable to ignore the warning. If not , how can it affect my resulting structure ? And are all such interaction "ignored for the rest of the simulation" ? So the system is unstable. Try minimizing with full interactions before doing anything funny with scaling. And I repeat my caution to you that trying to do an alchemical transformation of a peptide is a very unwise choice. You'll never get the simulations to converge in a practical amount of time. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Doubt about Free Energy control Minimization
Dear Justin, When the system is minimized with full interactions with no free energy code, I see no warnings and the systems is minimized properly. However, when the free energy code is added with couple-intramol = no, I encounter the said warning, but still the system can be minimized ignoring the warning. When the free energy code is added with couple-intramol = yes, there's no warning, but the system is again well minimized. I would like to learn if its reasonable to ignore the warning in the case where couple-intramol = no, since I am dealing with a peptide and intramolecular interactions can suppress the intermolecular interactions. I intend to perform normal-mode calculations on the resulting intermediates which are divergent from the Binding energy simulations requiring convergence. Hence, I presume there shouldn't be much complication in this case. I understand the approach seems quite outlandish, but still I aspire to execute the same. Any opinions and/or suggestions in this procedure will be greatly helpful. Many thanks, Bhagyesh. - Original Message - From: "Justin Lemkul" To: gmx-us...@gromacs.org Sent: Tuesday, June 27, 2017 6:42:33 PM Subject: Re: [gmx-users] Doubt about Free Energy control Minimization On 6/26/17 9:09 AM, Varvdekar Bhagyesh Rajendra wrote: > Dear Justin, > > I have encountered the following warning when I used the following code to > minimize my protein-ligand system when the interaction potential energy > between the protein and the ligand are multiplied by 0.9, 0.8, 0.7,..., 0.2, > 0.1. > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/Files/em_steep.mdp > > Warning: 1-4 interaction between 2263 and 2298 at distance 1.004 which is > larger than the 1-4 table size 1.000 nm > These are ignored for the rest of the simulation > This usually means your system is exploding, > if not, you should increase table-extension in your mdp file > or with user tables increase the table size > > > I suppose this error is due to setting couple-intramol = no. When it is set > to yes, the warning vanishes. > > But, this is my desired setting since, I do not intend to scale the intra > molecular interactions even though the ligand is a peptide. Is it reasonable > to ignore the warning. If not , how can it affect my resulting structure ? > And are all such interaction "ignored for the rest of the simulation" ? > So the system is unstable. Try minimizing with full interactions before doing anything funny with scaling. And I repeat my caution to you that trying to do an alchemical transformation of a peptide is a very unwise choice. You'll never get the simulations to converge in a practical amount of time. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Doubt about Free Energy control Minimization
On 6/26/17 9:09 AM, Varvdekar Bhagyesh Rajendra wrote: Dear Justin, I have encountered the following warning when I used the following code to minimize my protein-ligand system when the interaction potential energy between the protein and the ligand are multiplied by 0.9, 0.8, 0.7,..., 0.2, 0.1. http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/Files/em_steep.mdp Warning: 1-4 interaction between 2263 and 2298 at distance 1.004 which is larger than the 1-4 table size 1.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size I suppose this error is due to setting couple-intramol = no. When it is set to yes, the warning vanishes. But, this is my desired setting since, I do not intend to scale the intra molecular interactions even though the ligand is a peptide. Is it reasonable to ignore the warning. If not , how can it affect my resulting structure ? And are all such interaction "ignored for the rest of the simulation" ? So the system is unstable. Try minimizing with full interactions before doing anything funny with scaling. And I repeat my caution to you that trying to do an alchemical transformation of a peptide is a very unwise choice. You'll never get the simulations to converge in a practical amount of time. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Doubt about Free Energy control Minimization
Dear Justin, I have encountered the following warning when I used the following code to minimize my protein-ligand system when the interaction potential energy between the protein and the ligand are multiplied by 0.9, 0.8, 0.7,..., 0.2, 0.1. http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/Files/em_steep.mdp Warning: 1-4 interaction between 2263 and 2298 at distance 1.004 which is larger than the 1-4 table size 1.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size I suppose this error is due to setting couple-intramol = no. When it is set to yes, the warning vanishes. But, this is my desired setting since, I do not intend to scale the intra molecular interactions even though the ligand is a peptide. Is it reasonable to ignore the warning. If not , how can it affect my resulting structure ? And are all such interaction "ignored for the rest of the simulation" ? Apologies for the previous incomplete mail. Best Regards, Bhagyesh - Original Message - From: "Justin Lemkul" To: gmx-us...@gromacs.org Sent: Wednesday, June 14, 2017 4:50:58 AM Subject: Re: [gmx-users] Doubt about Free Energy control Minimization On 6/13/17 4:31 PM, Varvdekar Bhagyesh Rajendra wrote: > Dear Justin, > > I aspire to derive energy-minimum structures when the interaction potential > energy between the protein and the ligand are multiplied by 0.9, 0.8, > 0.7,..., 0.2, 0.1. > > I presume the following Free Energy minimization code mentioned in gromacs > tutorial may do the trick. I would appreciate if you could please verify if > it produces my intended result. > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/Files/em_steep.mdp > Possibly, but the outcomes may be unphysical. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Doubt about Free Energy control Minimization
Dear Justin, I have encountered the following error when I used the http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/Files/em_steep.mdp > Error: Warning: 1-4 interaction between 2263 and 2298 at distance 1.004 which is larger than the 1-4 table size 1.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size Best Regards, Bhagyesh - Original Message - From: "Justin Lemkul" To: gmx-us...@gromacs.org Sent: Wednesday, June 14, 2017 4:50:58 AM Subject: Re: [gmx-users] Doubt about Free Energy control Minimization On 6/13/17 4:31 PM, Varvdekar Bhagyesh Rajendra wrote: > Dear Justin, > > I aspire to derive energy-minimum structures when the interaction potential > energy between the protein and the ligand are multiplied by 0.9, 0.8, > 0.7,..., 0.2, 0.1. > > I presume the following Free Energy minimization code mentioned in gromacs > tutorial may do the trick. I would appreciate if you could please verify if > it produces my intended result. > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/Files/em_steep.mdp > Possibly, but the outcomes may be unphysical. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Doubt about Free Energy control Minimization
On 6/13/17 4:31 PM, Varvdekar Bhagyesh Rajendra wrote: Dear Justin, I aspire to derive energy-minimum structures when the interaction potential energy between the protein and the ligand are multiplied by 0.9, 0.8, 0.7,..., 0.2, 0.1. I presume the following Free Energy minimization code mentioned in gromacs tutorial may do the trick. I would appreciate if you could please verify if it produces my intended result. http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/Files/em_steep.mdp Possibly, but the outcomes may be unphysical. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Doubt about Free Energy control Minimization
Dear Justin, I aspire to derive energy-minimum structures when the interaction potential energy between the protein and the ligand are multiplied by 0.9, 0.8, 0.7,..., 0.2, 0.1. I presume the following Free Energy minimization code mentioned in gromacs tutorial may do the trick. I would appreciate if you could please verify if it produces my intended result. http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/Files/em_steep.mdp Thanking in anticipation, Best Regards, Bhagyesh -- 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.
