[gmx-users] gromacs.org_gmx-users Digest, Vol 176, Issue 11

Seketoulie Keretsu sekekeretsu at gmail.com
Fri Dec 7 06:56:57 CET 2018 

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
<gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
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> 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 +0000
> From: Benson Muite <benson.muite at ut.ee>
> To: "gromacs.org_gmx-users at maillist.sys.kth.se"
>         <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: Re: [gmx-users] numpy related problem in GROMACS
>         protein-ligand file preperation
> Message-ID: <2709ee01-b64b-acd2-0595-298bd7cad59f at 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 <module>
> >     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 <mehdi.bpour at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] How restrain the end-to-end distance in
>         simulation?
> Message-ID:
>         <CAM+zo1N90Kiy50ujwL4L6SuzD9SUGcLuyJipdQnnwV3vpzAAcw at mail.gmail.com>
> 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 <nedomacho at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] mdrun-adjusted cutoffs?!
> Message-ID: <8ffb83a0-4298-4dae-449a-65edad72bd9e at 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 <nedomacho at gmail.com wrote:
> >
> >> 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 <nedomacho at gmail.com wrote:
> >>>
> >>>> 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 <nedomacho at gmail.com wrote:
> >>>>>
> >>>>>> 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-request at 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
> >>>>
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> >>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >>>> send a mail to gmx-users-request at 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
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> >> send a mail to gmx-users-request at gromacs.org.
> >>
>
>
> ------------------------------
>
> Message: 4
> Date: Fri, 7 Dec 2018 15:38:55 +1100
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] mdrun-adjusted cutoffs?!
> Message-ID:
>         <CAMNuMAQND46EQ_moCpTUg4wicp5hAGm1FqStJcOBfo0ku263XQ at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> 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 <nedomacho at gmail.com wrote:
>
> > 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 <nedomacho at gmail.com wrote:
> > >
> > >> 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 <nedomacho at gmail.com wrote:
> > >>>
> > >>>> 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 <nedomacho at gmail.com wrote:
> > >>>>>
> > >>>>>> 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-request at 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-request at gromacs.org.
> > >>>>
> > >> --
> > >> Gromacs Users mailing list
> > >>
> > >> * Please search the archive at
> > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > >> posting!
> > >>
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> > >>
> > >> * For (un)subscribe requests visit
> > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > >> send a mail to gmx-users-request at gromacs.org.
> > >>
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
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> > posting!
> >
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> >
>
>
> ------------------------------
>
> --
> Gromacs Users mailing list
>
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> End of gromacs.org_gmx-users Digest, Vol 176, Issue 11
> ******************************************************

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