Re: [gmx-users] mdrun-adjusted cutoffs?!
I think that answers my question, thanks. :) On 12/6/2018 9:38 PM, Mark Abraham wrote: Hi, Zero, because we are shifting between equivalent ways to compute the total electrostatic interaction. You can turn off the PME tuning with mdrun -notunepme, but unless there's a bug, all that will do is force it to run slower than optimal. Obviously you could try it and see that the FE of hydration does not change with the model, so long as you have a reproducible protocol. Mark On Fri., 7 Dec. 2018, 06:39 Alex I'm not ignoring the long-range contribution, but yes, most of the effects I am talking about are short-range. What I am asking is how much the free energy of ionic hydration for K+ changes in, say, a system that contains KCl in bulk water -- with and without autotuning. Hence also the earlier question about being able to turn it off at least temporarily. Alex On 12/6/2018 5:42 AM, Mark Abraham wrote: Hi, It sounds like you are only looking at the short-ranged component of the electrostatic interaction, and thus ignoring the way the long range component also changes. Is the validity of the PME auto tuning the question at hand? Mark On Thu., 6 Dec. 2018, 21:09 Alex More specifically, electrostatics. For the stuff I'm talking about, the LJ portion contributes ~20% at the most. When the change in energetics is a statistically persistent value of order kT (of which about 20% comes from LJ), the quantity of interest (~exp(E/kT)) changes by a factor of 2.72. Again, this is a fairly special case, but I can easily envision someone doing ion permeation across KcsA and the currents would be similarly affected. For instance, when I set all cutoffs at 1.0 nm, mdrun ends up using something like 1.1 nm for electrostatics, at least that's what I see at the top of the log. I agree with what you said about vdW and it can be totally arbitraty and then often requires crutches elsewhere, but my question was whether for very sensitive quantities mdrun ends up utilizing the forcefield as it was designed and not in a "slightly off" regime. Basically, you asked me to describe our case and why I think there may be a slight issue, so there it is. Alex On 12/5/2018 10:34 PM, Mark Abraham wrote: Hi, One needs to be more specific than NB. There is evidence that VDW cutoffs of traditional lengths cause approximation errors that cause compensating parameterization errors elsewhere; those effects get worse if the system is inhomogeneous. Accordingly, mdrun never touches VDW cutoffs. Electrostatic with PME is quite another matter - there you need sufficient overall accuracy, and there are multiple equivalent ways to do that. Mark On Thu., 6 Dec. 2018, 09:56 Alex Hi Mark, I am not sure it is a concern, to be honest, so let me just lay out my thoughts and maybe you could share your opinion. I recently shared a link for our recent paper (https://www.nature.com/articles/s41563-018-0220-4), in which the quantity of interest is ion current via pores that disallow what we normally mean by diffusive permeation. Instead, there are considerable barriers and ionic currents are rather precisely described by exp(-E/kT), where E is some energy calculated from nonbonded interactions and includes a huge contribution from the solvent. It is my understanding that NB stuff gets parameterized at a particular cutoff value and our results are rather sensitive to that. I can't say we're dying to have extreme repeatability, but is it in your opinion acceptable to have variability in the cutoff radii and the rlist between something like 1.0 - 1.2 nm? To begin with, I am not particularly worried about it, because we mostly report on qualitative behaviors, but I am interested in your opinion. I have read the manual and unfortunately there is nothing in the way of actually showing estimates of NB energy variation as a function of small differences in cutoffs. Thank you, Alex On 12/5/2018 3:36 PM, Mark Abraham wrote: Hi, There's quite detailed discussion of the treatment of pair searching in section 3.4.2 of the reference manual. Perhaps that clarifies things? We're not aware of a reason to want to control things manually, but if you have one, we're keen to hear of it! Mark On Wed., 5 Dec. 2018, 09:59 Alex Hi all, We've long noticed that at the beginning of simulations mdrun goes through what seems like trying to adjust the short-range NB radii to its liking. What is up with that and does this mean that every simulation proceeds with a new cutoff? If so, is there a way to disable this? Thank you, Alex -- 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
[gmx-users] numpy related problem in GROMACS protein-ligand file preperation
Dear Seketoulie, Great. If replying to a digest, please change the subject so readers know what is useful. Regards, Benson On 12/7/18 7:12 AM, Seketoulie Keretsu wrote: > Dear > Thank you. > > "yum install numpy" worked for me. Surprised why i haven't tried that long > back. > On Fri, Dec 7, 2018 at 1:41 PM > wrote: >> Send gromacs.org_gmx-users mailing list submissions to >> gromacs.org_gmx-users@maillist.sys.kth.se >> >> To subscribe or unsubscribe via the World Wide Web, visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users >> or, via email, send a message with subject or body 'help' to >> gromacs.org_gmx-users-requ...@maillist.sys.kth.se >> >> You can reach the person managing the list at >> gromacs.org_gmx-users-ow...@maillist.sys.kth.se >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of gromacs.org_gmx-users digest..." >> >> >> Today's Topics: >> >>1. Re: numpy related problem in GROMACS protein-ligand file >> preperation (Benson Muite) >>2. How restrain the end-to-end distance in simulation? >> (Mehdi Bagherpour) >>3. Re: mdrun-adjusted cutoffs?! (Alex) >>4. Re: mdrun-adjusted cutoffs?! (Mark Abraham) >> >> >> -- >> >> Message: 1 >> Date: Thu, 6 Dec 2018 12:51:35 + >> From: Benson Muite >> To: "gromacs.org_gmx-users@maillist.sys.kth.se" >> >> Subject: Re: [gmx-users] numpy related problem in GROMACS >> protein-ligand file preperation >> Message-ID: <2709ee01-b64b-acd2-0595-298bd7cad...@ut.ee> >> Content-Type: text/plain; charset="utf-8" >> >> Hi Seketoulie, >> >> If you have administrator rights on a CentOS system >> >> sudo yum search numpy >> >> will let you know what numpy versions have already been packaged. >> >> You can also use >> >> pip install --user numpy >> >> or build from source: >> >> https://docs.scipy.org/doc/numpy-1.10.1/user/install.html >> >> Regards, >> >> Benson >> >> On 12/6/18 1:57 PM, Seketoulie Keretsu wrote: >>> Dear Experts, >>> >>> I am fairly new to gromacs (and linux CENTOS). I have recently >>> installed the Gromacs18 successfully. However while doing the >>> Protein-Lig tutorial I came across this problem while running the >>> python script: >>> >>> Traceback (most recent call last): >>> File "cgenff_charmm2gmx.py", line 46, in >>> import numpy as np >>> ImportError: No module named numpy >>> >>> >>> I have python 2.7.5 installed on my system. I am unable to find >>> solutions related to this. Kindly advise how to correct this? A hint >>> on the possible cause will be awesome too. >>> >>> Note: I also have Amber18 installed on my the same system which >>> apparently installs numpy. >>> >>> Thanking you. >>> >>> Sincerely, >>> Seketoulie >> >> -- >> >> Message: 2 >> Date: Thu, 6 Dec 2018 15:58:04 +0100 >> From: Mehdi Bagherpour >> To: gromacs.org_gmx-users@maillist.sys.kth.se >> Subject: [gmx-users] How restrain the end-to-end distance in >> simulation? >> Message-ID: >> >> Content-Type: text/plain; charset="UTF-8" >> >> Dear all, >> >> I am new in Gromacs and would like to restrain the the end-to-end distance >> of a bend DNA. I mean I want to restraint the distance between COM of end >> base-pairs in simulation. >> >> I would appreciate if you could let me know how to do that. >> >> Cheer, >> Mahdi >> >> >> -- >> >> Message: 3 >> Date: Thu, 6 Dec 2018 12:39:03 -0700 >> From: Alex >> To: gmx-us...@gromacs.org >> Subject: Re: [gmx-users] mdrun-adjusted cutoffs?! >> Message-ID: <8ffb83a0-4298-4dae-449a-65edad72b...@gmail.com> >> Content-Type: text/plain; charset=utf-8; format=flowed >> >> I'm not ignoring the long-range contribution, but yes, most of the >> effects I am talking about are short-range. What I am asking is how much >> the free energy of ionic hydration for K+ changes in, say, a system that >> contains KCl in bulk water -- with and without autotuning. Hence also >> the earlier question about being able to turn it off at least temporarily. >> >> Alex >> >> On 12/6/2018 5:42 AM, Mark Abraham wrote: >>> Hi, >>> >>> It sounds like you are only looking at the short-ranged component of the >>> electrostatic interaction, and thus ignoring the way the long range >>> component also changes. Is the validity of the PME auto tuning the question >>> at hand? >>> >>> Mark >>> >>> On Thu., 6 Dec. 2018, 21:09 Alex >> More specifically, electrostatics. For the stuff I'm talking about, the LJ portion contributes ~20% at the most. When the change in energetics is a statistically persistent value of order kT (of which about 20% comes from LJ), the quantity of interest (~exp(E/kT)) changes by a factor of 2.72. Again, this is a fairly special case, but I can easily envision someone doing ion permeation across KcsA and the currents would be
Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 176, Issue 11
Dear Thank you. "yum install numpy" worked for me. Surprised why i haven't tried that long back. On Fri, Dec 7, 2018 at 1:41 PM wrote: > > Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users@maillist.sys.kth.se > > To subscribe or unsubscribe via the World Wide Web, visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or, via email, send a message with subject or body 'help' to > gromacs.org_gmx-users-requ...@maillist.sys.kth.se > > You can reach the person managing the list at > gromacs.org_gmx-users-ow...@maillist.sys.kth.se > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gromacs.org_gmx-users digest..." > > > Today's Topics: > >1. Re: numpy related problem in GROMACS protein-ligand file > preperation (Benson Muite) >2. How restrain the end-to-end distance in simulation? > (Mehdi Bagherpour) >3. Re: mdrun-adjusted cutoffs?! (Alex) >4. Re: mdrun-adjusted cutoffs?! (Mark Abraham) > > > -- > > Message: 1 > Date: Thu, 6 Dec 2018 12:51:35 + > From: Benson Muite > To: "gromacs.org_gmx-users@maillist.sys.kth.se" > > Subject: Re: [gmx-users] numpy related problem in GROMACS > protein-ligand file preperation > Message-ID: <2709ee01-b64b-acd2-0595-298bd7cad...@ut.ee> > Content-Type: text/plain; charset="utf-8" > > Hi Seketoulie, > > If you have administrator rights on a CentOS system > > sudo yum search numpy > > will let you know what numpy versions have already been packaged. > > You can also use > > pip install --user numpy > > or build from source: > > https://docs.scipy.org/doc/numpy-1.10.1/user/install.html > > Regards, > > Benson > > On 12/6/18 1:57 PM, Seketoulie Keretsu wrote: > > Dear Experts, > > > > I am fairly new to gromacs (and linux CENTOS). I have recently > > installed the Gromacs18 successfully. However while doing the > > Protein-Lig tutorial I came across this problem while running the > > python script: > > > > Traceback (most recent call last): > > File "cgenff_charmm2gmx.py", line 46, in > > import numpy as np > > ImportError: No module named numpy > > > > > > I have python 2.7.5 installed on my system. I am unable to find > > solutions related to this. Kindly advise how to correct this? A hint > > on the possible cause will be awesome too. > > > > Note: I also have Amber18 installed on my the same system which > > apparently installs numpy. > > > > Thanking you. > > > > Sincerely, > > Seketoulie > > > -- > > Message: 2 > Date: Thu, 6 Dec 2018 15:58:04 +0100 > From: Mehdi Bagherpour > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: [gmx-users] How restrain the end-to-end distance in > simulation? > Message-ID: > > Content-Type: text/plain; charset="UTF-8" > > Dear all, > > I am new in Gromacs and would like to restrain the the end-to-end distance > of a bend DNA. I mean I want to restraint the distance between COM of end > base-pairs in simulation. > > I would appreciate if you could let me know how to do that. > > Cheer, > Mahdi > > > -- > > Message: 3 > Date: Thu, 6 Dec 2018 12:39:03 -0700 > From: Alex > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] mdrun-adjusted cutoffs?! > Message-ID: <8ffb83a0-4298-4dae-449a-65edad72b...@gmail.com> > Content-Type: text/plain; charset=utf-8; format=flowed > > I'm not ignoring the long-range contribution, but yes, most of the > effects I am talking about are short-range. What I am asking is how much > the free energy of ionic hydration for K+ changes in, say, a system that > contains KCl in bulk water -- with and without autotuning. Hence also > the earlier question about being able to turn it off at least temporarily. > > Alex > > On 12/6/2018 5:42 AM, Mark Abraham wrote: > > Hi, > > > > It sounds like you are only looking at the short-ranged component of the > > electrostatic interaction, and thus ignoring the way the long range > > component also changes. Is the validity of the PME auto tuning the question > > at hand? > > > > Mark > > > > On Thu., 6 Dec. 2018, 21:09 Alex > > >> More specifically, electrostatics. For the stuff I'm talking about, the > >> LJ portion contributes ~20% at the most. When the change in energetics > >> is a statistically persistent value of order kT (of which about 20% > >> comes from LJ), the quantity of interest (~exp(E/kT)) changes by a > >> factor of 2.72. Again, this is a fairly special case, but I can easily > >> envision someone doing ion permeation across KcsA and the currents would > >> be similarly affected. For instance, when I set all cutoffs at 1.0 nm, > >> mdrun ends up using something like 1.1 nm for electrostatics, at least > >> that's what I see at the top of the log. > >> > >> I agree with what you said about vdW and it can be totally arbitraty and > >> then
Re: [gmx-users] mdrun-adjusted cutoffs?!
Hi, Zero, because we are shifting between equivalent ways to compute the total electrostatic interaction. You can turn off the PME tuning with mdrun -notunepme, but unless there's a bug, all that will do is force it to run slower than optimal. Obviously you could try it and see that the FE of hydration does not change with the model, so long as you have a reproducible protocol. Mark On Fri., 7 Dec. 2018, 06:39 Alex I'm not ignoring the long-range contribution, but yes, most of the > effects I am talking about are short-range. What I am asking is how much > the free energy of ionic hydration for K+ changes in, say, a system that > contains KCl in bulk water -- with and without autotuning. Hence also > the earlier question about being able to turn it off at least temporarily. > > Alex > > On 12/6/2018 5:42 AM, Mark Abraham wrote: > > Hi, > > > > It sounds like you are only looking at the short-ranged component of the > > electrostatic interaction, and thus ignoring the way the long range > > component also changes. Is the validity of the PME auto tuning the > question > > at hand? > > > > Mark > > > > On Thu., 6 Dec. 2018, 21:09 Alex > > >> More specifically, electrostatics. For the stuff I'm talking about, the > >> LJ portion contributes ~20% at the most. When the change in energetics > >> is a statistically persistent value of order kT (of which about 20% > >> comes from LJ), the quantity of interest (~exp(E/kT)) changes by a > >> factor of 2.72. Again, this is a fairly special case, but I can easily > >> envision someone doing ion permeation across KcsA and the currents would > >> be similarly affected. For instance, when I set all cutoffs at 1.0 nm, > >> mdrun ends up using something like 1.1 nm for electrostatics, at least > >> that's what I see at the top of the log. > >> > >> I agree with what you said about vdW and it can be totally arbitraty and > >> then often requires crutches elsewhere, but my question was whether for > >> very sensitive quantities mdrun ends up utilizing the forcefield as it > >> was designed and not in a "slightly off" regime. Basically, you asked me > >> to describe our case and why I think there may be a slight issue, so > >> there it is. > >> > >> Alex > >> > >> On 12/5/2018 10:34 PM, Mark Abraham wrote: > >>> Hi, > >>> > >>> One needs to be more specific than NB. There is evidence that VDW > cutoffs > >>> of traditional lengths cause approximation errors that cause > compensating > >>> parameterization errors elsewhere; those effects get worse if the > system > >> is > >>> inhomogeneous. Accordingly, mdrun never touches VDW cutoffs. > >> Electrostatic > >>> with PME is quite another matter - there you need sufficient overall > >>> accuracy, and there are multiple equivalent ways to do that. > >>> > >>> Mark > >>> > >>> > >>> On Thu., 6 Dec. 2018, 09:56 Alex >>> > Hi Mark, > > I am not sure it is a concern, to be honest, so let me just lay out my > thoughts and maybe you could share your opinion. > > I recently shared a link for our recent paper > (https://www.nature.com/articles/s41563-018-0220-4), in which the > quantity of interest is ion current via pores that disallow what we > normally mean by diffusive permeation. Instead, there are considerable > barriers and ionic currents are rather precisely described by > exp(-E/kT), where E is some energy calculated from nonbonded > interactions and includes a huge contribution from the solvent. It is > my > understanding that NB stuff gets parameterized at a particular cutoff > value and our results are rather sensitive to that. I can't say we're > dying to have extreme repeatability, but is it in your opinion > acceptable to have variability in the cutoff radii and the rlist > between > something like 1.0 - 1.2 nm? To begin with, I am not particularly > worried about it, because we mostly report on qualitative behaviors, > but > I am interested in your opinion. I have read the manual and > unfortunately there is nothing in the way of actually showing > estimates > of NB energy variation as a function of small differences in cutoffs. > > Thank you, > > Alex > > > On 12/5/2018 3:36 PM, Mark Abraham wrote: > > Hi, > > > > There's quite detailed discussion of the treatment of pair searching > in > > section 3.4.2 of the reference manual. Perhaps that clarifies things? > We're > > not aware of a reason to want to control things manually, but if you > >> have > > one, we're keen to hear of it! > > > > Mark > > > > > > On Wed., 5 Dec. 2018, 09:59 Alex > > >> Hi all, > >> > >> We've long noticed that at the beginning of simulations mdrun goes > through > >> what seems like trying to adjust the short-range NB radii to its > >> liking. > >> What is up with that and does this mean that every simulation > proceeds
Re: [gmx-users] mdrun-adjusted cutoffs?!
I'm not ignoring the long-range contribution, but yes, most of the effects I am talking about are short-range. What I am asking is how much the free energy of ionic hydration for K+ changes in, say, a system that contains KCl in bulk water -- with and without autotuning. Hence also the earlier question about being able to turn it off at least temporarily. Alex On 12/6/2018 5:42 AM, Mark Abraham wrote: Hi, It sounds like you are only looking at the short-ranged component of the electrostatic interaction, and thus ignoring the way the long range component also changes. Is the validity of the PME auto tuning the question at hand? Mark On Thu., 6 Dec. 2018, 21:09 Alex More specifically, electrostatics. For the stuff I'm talking about, the LJ portion contributes ~20% at the most. When the change in energetics is a statistically persistent value of order kT (of which about 20% comes from LJ), the quantity of interest (~exp(E/kT)) changes by a factor of 2.72. Again, this is a fairly special case, but I can easily envision someone doing ion permeation across KcsA and the currents would be similarly affected. For instance, when I set all cutoffs at 1.0 nm, mdrun ends up using something like 1.1 nm for electrostatics, at least that's what I see at the top of the log. I agree with what you said about vdW and it can be totally arbitraty and then often requires crutches elsewhere, but my question was whether for very sensitive quantities mdrun ends up utilizing the forcefield as it was designed and not in a "slightly off" regime. Basically, you asked me to describe our case and why I think there may be a slight issue, so there it is. Alex On 12/5/2018 10:34 PM, Mark Abraham wrote: Hi, One needs to be more specific than NB. There is evidence that VDW cutoffs of traditional lengths cause approximation errors that cause compensating parameterization errors elsewhere; those effects get worse if the system is inhomogeneous. Accordingly, mdrun never touches VDW cutoffs. Electrostatic with PME is quite another matter - there you need sufficient overall accuracy, and there are multiple equivalent ways to do that. Mark On Thu., 6 Dec. 2018, 09:56 Alex Hi Mark, I am not sure it is a concern, to be honest, so let me just lay out my thoughts and maybe you could share your opinion. I recently shared a link for our recent paper (https://www.nature.com/articles/s41563-018-0220-4), in which the quantity of interest is ion current via pores that disallow what we normally mean by diffusive permeation. Instead, there are considerable barriers and ionic currents are rather precisely described by exp(-E/kT), where E is some energy calculated from nonbonded interactions and includes a huge contribution from the solvent. It is my understanding that NB stuff gets parameterized at a particular cutoff value and our results are rather sensitive to that. I can't say we're dying to have extreme repeatability, but is it in your opinion acceptable to have variability in the cutoff radii and the rlist between something like 1.0 - 1.2 nm? To begin with, I am not particularly worried about it, because we mostly report on qualitative behaviors, but I am interested in your opinion. I have read the manual and unfortunately there is nothing in the way of actually showing estimates of NB energy variation as a function of small differences in cutoffs. Thank you, Alex On 12/5/2018 3:36 PM, Mark Abraham wrote: Hi, There's quite detailed discussion of the treatment of pair searching in section 3.4.2 of the reference manual. Perhaps that clarifies things? We're not aware of a reason to want to control things manually, but if you have one, we're keen to hear of it! Mark On Wed., 5 Dec. 2018, 09:59 Alex Hi all, We've long noticed that at the beginning of simulations mdrun goes through what seems like trying to adjust the short-range NB radii to its liking. What is up with that and does this mean that every simulation proceeds with a new cutoff? If so, is there a way to disable this? Thank you, Alex -- 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
[gmx-users] How restrain the end-to-end distance in simulation?
Dear all, I am new in Gromacs and would like to restrain the the end-to-end distance of a bend DNA. I mean I want to restraint the distance between COM of end base-pairs in simulation. I would appreciate if you could let me know how to do that. Cheer, Mahdi -- 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] numpy related problem in GROMACS protein-ligand file preperation
Hi Seketoulie, If you have administrator rights on a CentOS system sudo yum search numpy will let you know what numpy versions have already been packaged. You can also use pip install --user numpy or build from source: https://docs.scipy.org/doc/numpy-1.10.1/user/install.html Regards, Benson On 12/6/18 1:57 PM, Seketoulie Keretsu wrote: > Dear Experts, > > I am fairly new to gromacs (and linux CENTOS). I have recently > installed the Gromacs18 successfully. However while doing the > Protein-Lig tutorial I came across this problem while running the > python script: > > Traceback (most recent call last): > File "cgenff_charmm2gmx.py", line 46, in > import numpy as np > ImportError: No module named numpy > > > I have python 2.7.5 installed on my system. I am unable to find > solutions related to this. Kindly advise how to correct this? A hint > on the possible cause will be awesome too. > > Note: I also have Amber18 installed on my the same system which > apparently installs numpy. > > Thanking you. > > Sincerely, > Seketoulie -- 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] numpy related problem in GROMACS protein-ligand file preperation
Dear Experts, I am fairly new to gromacs (and linux CENTOS). I have recently installed the Gromacs18 successfully. However while doing the Protein-Lig tutorial I came across this problem while running the python script: Traceback (most recent call last): File "cgenff_charmm2gmx.py", line 46, in import numpy as np ImportError: No module named numpy I have python 2.7.5 installed on my system. I am unable to find solutions related to this. Kindly advise how to correct this? A hint on the possible cause will be awesome too. Note: I also have Amber18 installed on my the same system which apparently installs numpy. Thanking you. Sincerely, Seketoulie -- 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] mdrun-adjusted cutoffs?!
Hi, It sounds like you are only looking at the short-ranged component of the electrostatic interaction, and thus ignoring the way the long range component also changes. Is the validity of the PME auto tuning the question at hand? Mark On Thu., 6 Dec. 2018, 21:09 Alex More specifically, electrostatics. For the stuff I'm talking about, the > LJ portion contributes ~20% at the most. When the change in energetics > is a statistically persistent value of order kT (of which about 20% > comes from LJ), the quantity of interest (~exp(E/kT)) changes by a > factor of 2.72. Again, this is a fairly special case, but I can easily > envision someone doing ion permeation across KcsA and the currents would > be similarly affected. For instance, when I set all cutoffs at 1.0 nm, > mdrun ends up using something like 1.1 nm for electrostatics, at least > that's what I see at the top of the log. > > I agree with what you said about vdW and it can be totally arbitraty and > then often requires crutches elsewhere, but my question was whether for > very sensitive quantities mdrun ends up utilizing the forcefield as it > was designed and not in a "slightly off" regime. Basically, you asked me > to describe our case and why I think there may be a slight issue, so > there it is. > > Alex > > On 12/5/2018 10:34 PM, Mark Abraham wrote: > > Hi, > > > > One needs to be more specific than NB. There is evidence that VDW cutoffs > > of traditional lengths cause approximation errors that cause compensating > > parameterization errors elsewhere; those effects get worse if the system > is > > inhomogeneous. Accordingly, mdrun never touches VDW cutoffs. > Electrostatic > > with PME is quite another matter - there you need sufficient overall > > accuracy, and there are multiple equivalent ways to do that. > > > > Mark > > > > > > On Thu., 6 Dec. 2018, 09:56 Alex > > >> Hi Mark, > >> > >> I am not sure it is a concern, to be honest, so let me just lay out my > >> thoughts and maybe you could share your opinion. > >> > >> I recently shared a link for our recent paper > >> (https://www.nature.com/articles/s41563-018-0220-4), in which the > >> quantity of interest is ion current via pores that disallow what we > >> normally mean by diffusive permeation. Instead, there are considerable > >> barriers and ionic currents are rather precisely described by > >> exp(-E/kT), where E is some energy calculated from nonbonded > >> interactions and includes a huge contribution from the solvent. It is my > >> understanding that NB stuff gets parameterized at a particular cutoff > >> value and our results are rather sensitive to that. I can't say we're > >> dying to have extreme repeatability, but is it in your opinion > >> acceptable to have variability in the cutoff radii and the rlist between > >> something like 1.0 - 1.2 nm? To begin with, I am not particularly > >> worried about it, because we mostly report on qualitative behaviors, but > >> I am interested in your opinion. I have read the manual and > >> unfortunately there is nothing in the way of actually showing estimates > >> of NB energy variation as a function of small differences in cutoffs. > >> > >> Thank you, > >> > >> Alex > >> > >> > >> On 12/5/2018 3:36 PM, Mark Abraham wrote: > >>> Hi, > >>> > >>> There's quite detailed discussion of the treatment of pair searching in > >>> section 3.4.2 of the reference manual. Perhaps that clarifies things? > >> We're > >>> not aware of a reason to want to control things manually, but if you > have > >>> one, we're keen to hear of it! > >>> > >>> Mark > >>> > >>> > >>> On Wed., 5 Dec. 2018, 09:59 Alex >>> > Hi all, > > We've long noticed that at the beginning of simulations mdrun goes > >> through > what seems like trying to adjust the short-range NB radii to its > liking. > What is up with that and does this mean that every simulation proceeds > >> with > a new cutoff? If so, is there a way to disable this? > > Thank you, > > Alex > -- > 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 >
Re: [gmx-users] Gmx distance
Did you try using gmx rdf -xy ? That is probably going to do what you want. You will have to ensure that the axis of the CNT is aligned exactly along the z axis. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu - When the only tool you own is a hammer, every problem begins to resemble a nail. On Mon, 26 Nov 2018 at 11:13, Dallas Warren wrote: > It will be calculating it based on the COM of the CNT, which will be a > single point, since that is what you are asking to do. > > One way I can see is align the axis of the CNT so that it has the same > x,y coordinates all the way along, process in same manner, then > separate the distance in the x-y plan from your output data using > simple trigonometry. Alternatively split box into slices along the > z-axis, so that the difference in the total distance at the top of the > slice versus middle of slice is sufficiently small (i.e. theta ~ 0), > calculate it for each slice, then average across all slices. > > Catch ya, > > Dr. Dallas Warren > Drug Delivery, Disposition and Dynamics > Monash Institute of Pharmaceutical Sciences, Monash University > 381 Royal Parade, Parkville VIC 3052 > dallas.war...@monash.edu > - > When the only tool you own is a hammer, every problem begins to resemble a > nail. > > On Thu, 22 Nov 2018 at 23:35, rose rahmani wrote: > > > > To be clear, i put 30 similar AA around NT i want to know how the average > > distance of group PROTEIN( consist of 30 AA ) varies during 100nS > > simulation. As i see in .gro file this distance decreased. I mean at the > > first moment i put them about 3nm far from Z axis of NT. THIS 3NM IS THE > > MINIMUM LENGTH OF A LINE BETWEEN AA COM POINT AND Z AXIS OF NT, AS YOU > CAN > > IMAGINE THIS LINE IS PERPENDICULAR TO Z AXIS OF NT. this length is > decrease > > after 100nS. But what i can't understand is that when i analyze it by > > g_dist( i select ZnS(NT) and Group Potein(=30 AA) in g_dist).. this is > the > > result! > > > > Group 0 ( System) has 27831 elements > > Group 1 ( Other) has 408 elements > > Group 2 (ZnS) has 408 elements > > Group 3 (Protein) has 720 elements > > Group 4 ( Protein-H) has 390 elements > > Group 5 (C-alpha) has30 elements > > Group 6 ( Backbone) has90 elements > > Group 7 ( MainChain) has90 elements > > Group 8 ( MainChain+Cb) has 120 elements > > Group 9 (MainChain+H) has 180 elements > > Group10 ( SideChain) has 540 elements > > Group11 (SideChain-H) has 300 elements > > Group12 (Prot-Masses) has 720 elements > > Group13 (non-Protein) has 27111 elements > > Group14 ( Water) has 26703 elements > > Group15 (SOL) has 26703 elements > > Group16 ( non-Water) has 1128 elements > > > > Select a group: 2 > > Selected 2: 'ZnS' > > Select a group: 3 > > Selected 3: 'Protein' > > > >0.0000.2176011 -0.0120678 -0.04654980.2122209 > >1.0000.2124534 -0.0301750 -0.04638700.2051198 > >2.0000.1923753 -0.0158403 -0.05101350.1848106 > >3.0000.1885315 -0.0107298 -0.04881600.1817856 > >4.0000.2044982 -0.0052650 -0.04903290.1984630 > >5.0000.2033602 -0.0002742 -0.04295370.1987720 > >6.0000.20504870.0013833 -0.04446580.2001646 > >7.0000.20024750.0041072 -0.04150030.1958568 > >8.0000.20064730.0033450 -0.05118890.1939790 > >9.0000.2032918 -0.119 -0.03300520.2005947 > > 10.0000.22556590.0003929 -0.04158570.2216990 > > 11.0000.22438110.0118313 -0.03447510.2214010 > > . > > . > > . > > 0.0000.6195676 -0.1357532 -0.00296350.6045051 > > 1.0000.5355353 -0.37166000.01250200.3853707 > > 2.0000.5243484 -0.36980010.01804520.3712997 > > 3.0000.4459361 -0.1407223 -0.20213220.3717511 > > 4.0000.5592619 -0.3545561 -0.21628430.3745463 > > 5.0000.5707593 -0.3472078 -0.23097590.3896961 > > 6.0000.5238984 -0.3467841 -0.01034190.3925600 > > 7.0000.5122938 -0.33790520.00978730.3849275 > > 8.0000.5608831 -0.3396225 -0.20521710.3963993 > > 9.0000.5230988 -0.34793640.01726030.3902240 > > 10.0000.5158455 -0.32838650.00471190.3977897 > > > > If the nanotube is along Z axis, so how g_dist calculate the COM of nano > > tube? Is it each point along Z axis which pass center of nano tube or COM > > in this case is just one point in the nanotube.
Re: [gmx-users] mdrun-adjusted cutoffs?!
More specifically, electrostatics. For the stuff I'm talking about, the LJ portion contributes ~20% at the most. When the change in energetics is a statistically persistent value of order kT (of which about 20% comes from LJ), the quantity of interest (~exp(E/kT)) changes by a factor of 2.72. Again, this is a fairly special case, but I can easily envision someone doing ion permeation across KcsA and the currents would be similarly affected. For instance, when I set all cutoffs at 1.0 nm, mdrun ends up using something like 1.1 nm for electrostatics, at least that's what I see at the top of the log. I agree with what you said about vdW and it can be totally arbitraty and then often requires crutches elsewhere, but my question was whether for very sensitive quantities mdrun ends up utilizing the forcefield as it was designed and not in a "slightly off" regime. Basically, you asked me to describe our case and why I think there may be a slight issue, so there it is. Alex On 12/5/2018 10:34 PM, Mark Abraham wrote: Hi, One needs to be more specific than NB. There is evidence that VDW cutoffs of traditional lengths cause approximation errors that cause compensating parameterization errors elsewhere; those effects get worse if the system is inhomogeneous. Accordingly, mdrun never touches VDW cutoffs. Electrostatic with PME is quite another matter - there you need sufficient overall accuracy, and there are multiple equivalent ways to do that. Mark On Thu., 6 Dec. 2018, 09:56 Alex Hi Mark, I am not sure it is a concern, to be honest, so let me just lay out my thoughts and maybe you could share your opinion. I recently shared a link for our recent paper (https://www.nature.com/articles/s41563-018-0220-4), in which the quantity of interest is ion current via pores that disallow what we normally mean by diffusive permeation. Instead, there are considerable barriers and ionic currents are rather precisely described by exp(-E/kT), where E is some energy calculated from nonbonded interactions and includes a huge contribution from the solvent. It is my understanding that NB stuff gets parameterized at a particular cutoff value and our results are rather sensitive to that. I can't say we're dying to have extreme repeatability, but is it in your opinion acceptable to have variability in the cutoff radii and the rlist between something like 1.0 - 1.2 nm? To begin with, I am not particularly worried about it, because we mostly report on qualitative behaviors, but I am interested in your opinion. I have read the manual and unfortunately there is nothing in the way of actually showing estimates of NB energy variation as a function of small differences in cutoffs. Thank you, Alex On 12/5/2018 3:36 PM, Mark Abraham wrote: Hi, There's quite detailed discussion of the treatment of pair searching in section 3.4.2 of the reference manual. Perhaps that clarifies things? We're not aware of a reason to want to control things manually, but if you have one, we're keen to hear of it! Mark On Wed., 5 Dec. 2018, 09:59 Alex Hi all, We've long noticed that at the beginning of simulations mdrun goes through what seems like trying to adjust the short-range NB radii to its liking. What is up with that and does this mean that every simulation proceeds with a new cutoff? If so, is there a way to disable this? Thank you, Alex -- 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.
Re: [gmx-users] [ implicit_genborn_params ] for Gromos54a7 FF
Den 2018-12-04 kl. 22:49, skrev Alex: Hi David, Thank you. On Tue, Dec 4, 2018 at 4:24 PM David van der Spoel wrote: Den 2018-12-04 kl. 21:58, skrev Alex: Dear all. I wonder where the [ implicit_genborn_params ] section should come in the below topol.top file for which the Gromos54a7 force fields are used? For the Amber and OPLS-FF I notice that all the [ implicit_genborn_params ] parameters are in a gbsa.itp file but that was not the case for Gromos54a7 and even it did not worked when I created a gbsa.itp for for gromos5a7. Please note first that only the 4.5 and 4.6 branches of gromacs run generalized born efficiently and reliably (as far as I know). I didn't know that, I use the 2018.2 version and at least the tpr file can be produced ... . Second, if there is no predefined force field you should not make an ad-hoc one but use a well-defined one instead. Third, why bother with generalized born at all? There are so many papers showing that the predictive power is poor that it will be hard to defend any results based on it. If non of Still, HCT and OBC, then what else you would suggest that has been implemented in Gromacs and could be used easily in Gromacs? I just wanted to see the diffusion and adsorption of some polymers to solid surface. The process is so slow in explicit water and I just wanted to see it the polymer come to the surface at all! However I see too much force in the slab with the current [ implicit_genborn_params ] parameter which I have used for now. For qualitative work it is fine, although there is basically no correlation between explicit solvent and implicit solvent for solvation energies (e.g. J. Chem. Theory Comput. 13 pp. 1034-1043 (2017)). This means that even if your polymer adsorbs to the surface, it may be unphysical. BTW, meanwhile I found that the [ implicit_genborn_params ] should come immediatly after the [ atomtypes ] section in topol.top file. Regards, Alex %-TOP--- #include "/u/alex/.local/gromos54a7.ff/forcefield.itp" ; #include "A.itp" #include "B.itp" #include "C.itp" ; [ system ] A-B-C in implicit water [ molecules ] A 1 B 29 C 14 B 29 C 14 %-- Thank you Regards, Alex -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- 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. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- 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.
