[gmx-users] numpy related problem in GROMACS protein-ligand file preperation

Benson Muite benson.muite at ut.ee
Fri Dec 7 07:01:13 CET 2018 

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
> <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
>>>>>>
>>>>>> * 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.
>>>>
>>
>> ------------------------------
>>
>> 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!
>>>>>
>>>>> * 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
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>> End of gromacs.org_gmx-users Digest, Vol 176, Issue 11
>> ******************************************************

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