Re: [gmx-users] How to create a spherocylindrical wall

[Jagannath Mondal]

Hi
  This dates back to an old query on using restraints to create a
spherocylindricalconfinement.

  a) Based on previous suggestions, we were exploring the options of
flatbottomed potential.
   However, it has three options only: sphere, cylinder and layer. We
wanted to create a combination of cylinder and (hemi)sphere to make a
 hollow spherocylinder. But we do not find how to make the hemisphere using
flatbottomed potential.
  Also, we wanted to have the centers of cylinder and sphere in  different
locations. However, we are not sure within the current gromacs
implementation, how we can have two different centers for flat-bottomed
restraints.

b) In worse case scenario, we were thinking of modifying the source code of
gromacs flat-bottomed restraints to have the option of
spherocylindrical restraints.
In that case, can some one point out the relevant locations of source code
for flat-bottomed potential withing gromacs 5.x installation directory?


On Sat, Sep 12, 2015 at 7:52 AM, Barnett, James W 
wrote:

> On Fri, 2015-09-11 at 11:57 +0530, Jagannath Mondal wrote:
> > Hi
> >   I would like to perform a simulation ( without any periodic
> > boundary
> > condition) where I need to have a wall of spherocylindrical geometry.
> > In
> > other words the particles will be confined inside a spherocylinder.
> >
> >  Is there any good suggestion on how to achieve that in gromacs?
> >
> > 1) One option I thought of achieving that is by having a
> > spherocylindrical
> > wall potential.  Is there a way of putting the wall potential in the
> > form
> > of a table-potential ? (Not sure cylinder option in gromacs umbrella
> > sampling  not going to be helpful).
>
> This might be do-able and would not require a table potential. Check
> out flat-bottom restraints in section 4.3.2 in the reference (PDF)
> manual.
>
> >
> > 2)  Or,should I put a bunch of hard sphere which constitute the
> > spherocylindrical boundary so that the particles inside the
> > spherocylinder
> > will have a repulsive interaction each time they come towards the
> > boundary ?
>
> I'm not sure how you would implement this in a simple way with GROMACS.
>
>
> --
> James “Wes” Barnett, Ph.D. Candidate
> Louisiana Board of Regents Fellow
>
> Chemical and Biomolecular Engineering
> Tulane University
> 341-B Lindy Boggs Center for Energy and Biotechnology
> 6823 St. Charles Ave
> New Orleans, Louisiana 70118-5674
> jbarn...@tulane.ed
> --
> 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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Re: [gmx-users] How to create a spherocylindrical wall

[jagannath mondal]

Hi
  This dates back to an old query on using restraints to create a
spherocylindrical confinement.

  a) Based on previous suggestions, we were exploring the options of
flatbottomed potential.
   However, it has three options only: sphere, cylinder and layer. We
wanted to create a combination of cylinder and (hemi)sphere to make a
 hollow spherocylinder. But we do not find how to make the hemisphere using
flatbottomed potential.
  Also, we wanted to have the centers of cylinder and sphere in  different
locations. However, we are not sure within the current gromacs
implementation, how we can have two different centers for flat-bottomed
restraints.

b) In worse case scenario, we were thinking of modifying the source code of
gromacs flat-bottomed restraints to have the option of spherocylindrical
restraints. In that case, can some one point out the relevant locations of
source code for flat-bottomed potential withing gromacs 5.x installation
directory?

Thanks
Jagannath

On Sat, Sep 12, 2015 at 7:52 AM, Barnett, James W 
wrote:

> On Fri, 2015-09-11 at 11:57 +0530, Jagannath Mondal wrote:
> > Hi
> >   I would like to perform a simulation ( without any periodic
> > boundary
> > condition) where I need to have a wall of spherocylindrical geometry.
> > In
> > other words the particles will be confined inside a spherocylinder.
> >
> >  Is there any good suggestion on how to achieve that in gromacs?
> >
> > 1) One option I thought of achieving that is by having a
> > spherocylindrical
> > wall potential.  Is there a way of putting the wall potential in the
> > form
> > of a table-potential ? (Not sure cylinder option in gromacs umbrella
> > sampling  not going to be helpful).
>
> This might be do-able and would not require a table potential. Check
> out flat-bottom restraints in section 4.3.2 in the reference (PDF)
> manual.
>
> >
> > 2)  Or,should I put a bunch of hard sphere which constitute the
> > spherocylindrical boundary so that the particles inside the
> > spherocylinder
> > will have a repulsive interaction each time they come towards the
> > boundary ?
>
> I'm not sure how you would implement this in a simple way with GROMACS.
>
>
> --
> James “Wes” Barnett, Ph.D. Candidate
> Louisiana Board of Regents Fellow
>
> Chemical and Biomolecular Engineering
> Tulane University
> 341-B Lindy Boggs Center for Energy and Biotechnology
> 6823 St. Charles Ave
> New Orleans, Louisiana 70118-5674
> jbarn...@tulane.ed
> --
> 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.
-- 
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Re: [gmx-users] simulation_time

[Ms. Nikita Bora]

 Original Message 
Subject: Re: simulation_time
From:"Ms. Nikita Bora" 
Date:Mon, May 16, 2016 9:42 am
To:  nik...@tezu.ernet.in
--

Respected Sir,

Thanks for the reply. I would further like to know that according to this
tutorial
(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/07_equil2.html)
the rvdw=rcoulomb=1 is used for the protein while according to this
tutorial
(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/07_equil2.html)
rvdw=rcoulomb=1.4 is used. why a different value for the simple protein
and protein-ligand complex is used??


> Respected Sir,
>
> Recently i followed your tutorial for simulation of a 50 ns final mdrun
of protein-ligand complex where the value of rvdw=rcoulomb=1.4 was used.
The simulation runned at aorund 10 ns/day . While for the same  complex
when rvdw=rcoulomb=1 is made the run was 10 ns/day.
>
> Sir i would like to know is there any standard value for rvdw,rcoulomb
and why a longer time is taken for 1.4 value
>
>
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Re: [gmx-users] Restart simulation from checkpoint file with fewer nodes

[jkrieger]

ok thanks

> Hi,
>
> Yes, that's one way to work around the problem. In some places, a module
> subsystem can be used to take care of the selection automatically, but you
> don't want to set one up for just you to use.
>
> Mark
>
> On Sun, May 15, 2016 at 11:48 AM  wrote:
>
>> Thanks Mark,
>>
>> My sysadmins have let me install my own GROMACS versions and have not
>> informed me of any such mechanism. Would you suggest I qrsh into a node
>> of
>> each type and build an mdrun-only version on each? I'd then select a
>> particular node type for a submit script with the relevant mdrun.
>>
>> Many thanks
>> James
>>
>> > Hi,
>> >
>> > On Sat, May 14, 2016 at 1:09 PM  wrote:
>> >
>> >> In case it's relevant/interesting to anyone, here are the details on
>> our
>> >> cluster nodes:
>> >>
>> >> nodes   #   model   # cores cpu
>> >> model
>> >>   RAM   node_type
>> >> fmb01 - fmb33   33  IBM HS21XM  8   3 GHz
>> >> Xeon
>> >> E5450
>> >>  16GB   hs21
>> >> fmb34 - fmb42   9   IBM HS228   2.4
>> GHz
>> >> Xeon E5530
>> >> 16GBhs22
>> >> fmb43 - fmb88   45  Dell PE M6108   2.4
>> GHz
>> >> Xeon E5530
>> >>  16GB   m610
>> >> fmb88 - fmb90   3   Dell PE M610+   12  3.4
>> GHz
>> >> Xeon X5690
>> >>   48GB  m610+
>> >> fmb91 - fmb202  112 Dell PE M62024 (HT) 2.9
>> GHz
>> >> Xeon E5-2667
>> >>64GB m620
>> >> fmb203 - fmb279 77  Dell PE M62024 (HT) 3.5
>> GHz
>> >> Xeon E5-2643 v2 64GB
>> >> m620+
>> >> fmb280 - fmb359 80  Dell PE M63024 (HT) 3.4
>> GHz
>> >> Xeon E5-2643 v3 64GB
>> >> m630
>> >>
>> >> I could only run GROMACS 4.6.2 on the last three node types and I
>> >> believe
>> >> the same is true for 5.0.4
>> >>
>> >
>> > Sure. GROMACS is designed to target whichever hardware was selected at
>> > configure time, which your sysadmins for such a heterogeneous cluster
>> > should have documented somewhere. They should also be making available
>> to
>> > you a mechanism to target your jobs to nodes where they can run
>> programs
>> > that use the hardware efficiently, or providing GROMACS installations
>> that
>> > work regardless of which node you are actually on. You might like to
>> > respectfully remind them of the things we say at
>> >
>> http://manual.gromacs.org/documentation/5.1.2/install-guide/index.html#portability-aspects
>> > (These thoughts are common to earlier versions also.)
>> >
>> > Mark
>> >
>> >
>> > Best wishes
>> >> James
>> >>
>> >> > I have found that only some kinds of nodes on our cluster work for
>> >> gromacs
>> >> > 4.6 (the ones we call m620, m620+ and m630 but not others - I can
>> >> check
>> >> > the details tomorrow). I haven't tested it again now I'm using 5.0
>> so
>> >> > don't know if that's still an issue but if it is it could explain
>> why
>> >> your
>> >> > restart failed even and the initial run didn't.
>> >> >
>> >> >> thanks a lot for your fast response.
>> >> >>
>> >> >> I have tried it, and it failed. I ask in this forum just to make
>> >> sure.
>> >> >> However, there was something in my cluster that probably make it
>> >> failed.
>> >> >> I'll handle it first and then retry to restart again.
>> >> >>
>> >> >> Regards,
>> >> >>
>> >> >> Husen
>> >> >>
>> >> >> On Sat, May 14, 2016 at 7:58 AM, Justin Lemkul 
>> >> wrote:
>> >> >>
>> >> >>>
>> >> >>>
>> >> >>> On 5/13/16 8:53 PM, Husen R wrote:
>> >> >>>
>> >>  Dear all
>> >> 
>> >>  Does simulation able to be restarted from checkpoint file with
>> >> fewer
>> >>  nodes ?
>> >>  let's say, at the first time, I run simulation with 3 nodes. At
>> >>  running
>> >>  time, one of those nodes is crashed and the simulation is
>> >> terminated.
>> >> 
>> >>  I want to restart that simulation immadiately based on
>> checkpoint
>> >> file
>> >>  with
>> >>  the remaining 2 nodes. does gromacs support such case ?
>> >>  I need help.
>> >> 
>> >> >>>
>> >> >>> Have you tried it?  It should work.  You will probably get a note
>> >> about
>> >> >>> the continuation not being exact due to a change in the number of
>> >> >>> cores,
>> >> >>> but the run should proceed fine.
>> >> >>>
>> >> >>> -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
>> >> 

Re: [gmx-users] error in running mdrun of membrane protein in a mixed bilayer with MARTINI MODEL

[Justin Lemkul]

Please don't reply to entire digests.

On 5/15/16 4:48 AM, Antara mazumdar wrote:

Dear Justin,

I am using the velocities from the NPT run. Could you please explain on the
.cpt file you mentioned?



This command:

gmx grompp -c step6.6equilibration.gro -p system.top -n new_index.ndx -f
MD.mdp -o MD.tpr

might preserve the low-precision velocities written to the .gro file, but it 
preserves nothing about the ensemble at the end of the equilibration run. 
Consult any basic tutorial for proper usage of grompp and continuing runs.  If 
you don't carefully continue your simulations, you're going to find all sorts of 
bizarre behavior.


-Justin


Kind Regards,
Antara

--
Junior research fellow(project)
Systems biology group
CSIR-Institute of Genomics & Integrative Biology
South Campus
New Delhi -  110020
M : +91-9717970040
--



On Sun, May 15, 2016 at 10:51 AM, <
gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote:


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Today's Topics:

   1. COM-Pull along a direction (Pengzhi Zhang)
   2. Re: error in running mdrun of membrane protein in a mixed
  bilayer with MARTINI MODEL (Justin Lemkul)
   3. Umbrella Sampling - choice of pull-coord?-dim (Lukas Zimmermann)
   4. PCA and FEL (sun)
   5. Re: PCA and FEL (Tsjerk Wassenaar)


--

Message: 1
Date: Sat, 14 May 2016 14:58:37 -0500
From: Pengzhi Zhang 
To: 
Subject: [gmx-users] COM-Pull along a direction
Message-ID: <5737836d.8010...@central.uh.edu>
Content-Type: text/plain; charset="utf-8"; format=flowed

Dear Gromacs users,

I am trying to pull an ion out of a protein using Gromacs/5.0.4. I pull
the ion along specific pre-determined paths.

 From my understanding, pulling along a direction _V guarantees that the
dumb bead would move only at direction _V. The position of the dumb bead
is simply: _r(t) = _r(0) + _V*speed*time (_ means vector). And if the
spring constant is sufficiently large, the pulled atom (a single ion)
would also follow the dumb bead (with fluctuations). However, I found
that no matter how large the spring constant is (I vary it from 100 to
1,000,000 kJ/mol/nm**2), the pulled atom deviates from the direction _V
in a certain amount of time (usually after the pulled bead unbinds),
sometimes it even goes perpendicular to _V and moves out of the box,
terminating the simulation.

Does the direction _V (pull-coord1-vec) mean the direction of
instantaneous pull force or the direction of the path that the dumb bead
follows?

Thank you very much in advance!


Here is the pull part of my mdp file.
; COM PULLING
; Pull type: no, umbrella, constraint or constant-force
pull= umbrella
pull-geometry= direction
pull-ngroups  = 2
pull-ncoords  = 1
pull-group1-name  = binding_site_atoms
pull-group2-name  = pull_ion   ; pull group
pull-start= yes
pull-coord1-vec  = -0.07 -0.04 0.99
pull-coord1-groups= 1 2
pull_coord1_rate= 0.001; nm/ps
pull-coord1-k = 1   ; kJ/mol/nm^2
pull-nstxout   = 10 ; 0.02 ps
pull-nstfout= 10
pull-print-reference= yes


Sincerely,
Pengzhi


--

Message: 2
Date: Sat, 14 May 2016 18:33:08 -0400
From: Justin Lemkul 
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] error in running mdrun of membrane protein in
a mixed bilayer with MARTINI MODEL
Message-ID: <5b732333-0517-e66f-2e4b-7a9cf337e...@vt.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed



On 5/14/16 2:34 PM, Mark Abraham wrote:

Hi,

Please keep the discussion on the mailing list, so others can help and
learn.


Antara said:
I have pasted the mdrun command i used to run it in parallel with the

number of processors i used which was 16. The command is :



/app/setups/gromacs-5.1.1/build/bin -deffnm MD -pin on -rdd 1.8


That still isn't a command you've copied and pasted from a terminal or a
script. You needed a call that might include mpirun -np 16 gmx_mpi mdrun,
etc.


In the pbs script, i used 16 in the number of processors option.


What happens when you run on one rank?


For the production tpr, i used the gro file from the last equilibration

step(step6.6) The command used was :


gmx grompp -c 

Re: [gmx-users] Restart simulation from checkpoint file with fewer nodes

[Mark Abraham]

Hi,

Yes, that's one way to work around the problem. In some places, a module
subsystem can be used to take care of the selection automatically, but you
don't want to set one up for just you to use.

Mark

On Sun, May 15, 2016 at 11:48 AM  wrote:

> Thanks Mark,
>
> My sysadmins have let me install my own GROMACS versions and have not
> informed me of any such mechanism. Would you suggest I qrsh into a node of
> each type and build an mdrun-only version on each? I'd then select a
> particular node type for a submit script with the relevant mdrun.
>
> Many thanks
> James
>
> > Hi,
> >
> > On Sat, May 14, 2016 at 1:09 PM  wrote:
> >
> >> In case it's relevant/interesting to anyone, here are the details on our
> >> cluster nodes:
> >>
> >> nodes   #   model   # cores cpu
> >> model
> >>   RAM   node_type
> >> fmb01 - fmb33   33  IBM HS21XM  8   3 GHz
> >> Xeon
> >> E5450
> >>  16GB   hs21
> >> fmb34 - fmb42   9   IBM HS228   2.4 GHz
> >> Xeon E5530
> >> 16GBhs22
> >> fmb43 - fmb88   45  Dell PE M6108   2.4 GHz
> >> Xeon E5530
> >>  16GB   m610
> >> fmb88 - fmb90   3   Dell PE M610+   12  3.4 GHz
> >> Xeon X5690
> >>   48GB  m610+
> >> fmb91 - fmb202  112 Dell PE M62024 (HT) 2.9 GHz
> >> Xeon E5-2667
> >>64GB m620
> >> fmb203 - fmb279 77  Dell PE M62024 (HT) 3.5 GHz
> >> Xeon E5-2643 v2 64GB
> >> m620+
> >> fmb280 - fmb359 80  Dell PE M63024 (HT) 3.4 GHz
> >> Xeon E5-2643 v3 64GB
> >> m630
> >>
> >> I could only run GROMACS 4.6.2 on the last three node types and I
> >> believe
> >> the same is true for 5.0.4
> >>
> >
> > Sure. GROMACS is designed to target whichever hardware was selected at
> > configure time, which your sysadmins for such a heterogeneous cluster
> > should have documented somewhere. They should also be making available to
> > you a mechanism to target your jobs to nodes where they can run programs
> > that use the hardware efficiently, or providing GROMACS installations
> that
> > work regardless of which node you are actually on. You might like to
> > respectfully remind them of the things we say at
> >
> http://manual.gromacs.org/documentation/5.1.2/install-guide/index.html#portability-aspects
> > (These thoughts are common to earlier versions also.)
> >
> > Mark
> >
> >
> > Best wishes
> >> James
> >>
> >> > I have found that only some kinds of nodes on our cluster work for
> >> gromacs
> >> > 4.6 (the ones we call m620, m620+ and m630 but not others - I can
> >> check
> >> > the details tomorrow). I haven't tested it again now I'm using 5.0 so
> >> > don't know if that's still an issue but if it is it could explain why
> >> your
> >> > restart failed even and the initial run didn't.
> >> >
> >> >> thanks a lot for your fast response.
> >> >>
> >> >> I have tried it, and it failed. I ask in this forum just to make
> >> sure.
> >> >> However, there was something in my cluster that probably make it
> >> failed.
> >> >> I'll handle it first and then retry to restart again.
> >> >>
> >> >> Regards,
> >> >>
> >> >> Husen
> >> >>
> >> >> On Sat, May 14, 2016 at 7:58 AM, Justin Lemkul 
> >> wrote:
> >> >>
> >> >>>
> >> >>>
> >> >>> On 5/13/16 8:53 PM, Husen R wrote:
> >> >>>
> >>  Dear all
> >> 
> >>  Does simulation able to be restarted from checkpoint file with
> >> fewer
> >>  nodes ?
> >>  let's say, at the first time, I run simulation with 3 nodes. At
> >>  running
> >>  time, one of those nodes is crashed and the simulation is
> >> terminated.
> >> 
> >>  I want to restart that simulation immadiately based on checkpoint
> >> file
> >>  with
> >>  the remaining 2 nodes. does gromacs support such case ?
> >>  I need help.
> >> 
> >> >>>
> >> >>> Have you tried it?  It should work.  You will probably get a note
> >> about
> >> >>> the continuation not being exact due to a change in the number of
> >> >>> cores,
> >> >>> but the run should proceed fine.
> >> >>>
> >> >>> -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
> >> >>> 

Re: [gmx-users] How to visualize the Free Energy Landscape file generated by g_sham

[sun]

You can convert xpm2txt and plot in Origin as well

Sent from my iPhone

> On 29-Jan-2014, at 11:21 am, tarak karmakar  wrote:
> 
> Hi Monoj,
> 
> You can use GNU 3D plot for this particular case.
> 
> cheers,
> Tarak
> 
> 
> On Wed, Jan 29, 2014 at 8:02 AM, Monoj Mon Kalita 
> wrote:
> 
>> Dear Gromacs user,
>> 
>> I have used the g_sham method to generate free-energy-landscape.xpm file.
>> To do that I have followed this website
>> 
>> http://nmr.chem.uu.nl/~adrien/course/molmod/analysis2.html
>> 
>> Now my problem is how to plot RMSD, radius of gyration and free energy in a
>> single file . I can have a plot of Rg and RMSD in 2D, but unable to plot
>> Rg, RMSD and Free energy value in a single file as they have shown in the
>> website. I have used the mathematica software version 9 and have used the
>> notepad given by the website. When I execute the program it doesn't show
>> any output. Is there any other way to have a nice plot of Rg, RMSD and Free
>> energy together in a single polt? Have a nice day.
>> 
>> --
>> 
>> With Regards
>> Monoj Mon Kalita
>> Institute of Biophotonics<
>> http://www.ym.edu.tw/biophotonics/eng_version/home.htm>
>> Fischer's Lab 
>> National Yang-Ming University<
>> http://nymu-e.web.ym.edu.tw/front/bin/home.phtml>
>> Taipei, Taiwan
>> mon.123c...@gmail.com
>> +886-981702268
>> --
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Re: [gmx-users] Restart simulation from checkpoint file with fewer nodes

[jkrieger]

Thanks Mark,

My sysadmins have let me install my own GROMACS versions and have not
informed me of any such mechanism. Would you suggest I qrsh into a node of
each type and build an mdrun-only version on each? I'd then select a
particular node type for a submit script with the relevant mdrun.

Many thanks
James

> Hi,
>
> On Sat, May 14, 2016 at 1:09 PM  wrote:
>
>> In case it's relevant/interesting to anyone, here are the details on our
>> cluster nodes:
>>
>> nodes   #   model   # cores cpu
>> model
>>   RAM   node_type
>> fmb01 - fmb33   33  IBM HS21XM  8   3 GHz
>> Xeon
>> E5450
>>  16GB   hs21
>> fmb34 - fmb42   9   IBM HS228   2.4 GHz
>> Xeon E5530
>> 16GBhs22
>> fmb43 - fmb88   45  Dell PE M6108   2.4 GHz
>> Xeon E5530
>>  16GB   m610
>> fmb88 - fmb90   3   Dell PE M610+   12  3.4 GHz
>> Xeon X5690
>>   48GB  m610+
>> fmb91 - fmb202  112 Dell PE M62024 (HT) 2.9 GHz
>> Xeon E5-2667
>>64GB m620
>> fmb203 - fmb279 77  Dell PE M62024 (HT) 3.5 GHz
>> Xeon E5-2643 v2 64GB
>> m620+
>> fmb280 - fmb359 80  Dell PE M63024 (HT) 3.4 GHz
>> Xeon E5-2643 v3 64GB
>> m630
>>
>> I could only run GROMACS 4.6.2 on the last three node types and I
>> believe
>> the same is true for 5.0.4
>>
>
> Sure. GROMACS is designed to target whichever hardware was selected at
> configure time, which your sysadmins for such a heterogeneous cluster
> should have documented somewhere. They should also be making available to
> you a mechanism to target your jobs to nodes where they can run programs
> that use the hardware efficiently, or providing GROMACS installations that
> work regardless of which node you are actually on. You might like to
> respectfully remind them of the things we say at
> http://manual.gromacs.org/documentation/5.1.2/install-guide/index.html#portability-aspects
> (These thoughts are common to earlier versions also.)
>
> Mark
>
>
> Best wishes
>> James
>>
>> > I have found that only some kinds of nodes on our cluster work for
>> gromacs
>> > 4.6 (the ones we call m620, m620+ and m630 but not others - I can
>> check
>> > the details tomorrow). I haven't tested it again now I'm using 5.0 so
>> > don't know if that's still an issue but if it is it could explain why
>> your
>> > restart failed even and the initial run didn't.
>> >
>> >> thanks a lot for your fast response.
>> >>
>> >> I have tried it, and it failed. I ask in this forum just to make
>> sure.
>> >> However, there was something in my cluster that probably make it
>> failed.
>> >> I'll handle it first and then retry to restart again.
>> >>
>> >> Regards,
>> >>
>> >> Husen
>> >>
>> >> On Sat, May 14, 2016 at 7:58 AM, Justin Lemkul 
>> wrote:
>> >>
>> >>>
>> >>>
>> >>> On 5/13/16 8:53 PM, Husen R wrote:
>> >>>
>>  Dear all
>> 
>>  Does simulation able to be restarted from checkpoint file with
>> fewer
>>  nodes ?
>>  let's say, at the first time, I run simulation with 3 nodes. At
>>  running
>>  time, one of those nodes is crashed and the simulation is
>> terminated.
>> 
>>  I want to restart that simulation immadiately based on checkpoint
>> file
>>  with
>>  the remaining 2 nodes. does gromacs support such case ?
>>  I need help.
>> 
>> >>>
>> >>> Have you tried it?  It should work.  You will probably get a note
>> about
>> >>> the continuation not being exact due to a change in the number of
>> >>> cores,
>> >>> but the run should proceed fine.
>> >>>
>> >>> -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 

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 145, Issue 55

[Antara mazumdar]

Dear Justin,

I am using the velocities from the NPT run. Could you please explain on the
.cpt file you mentioned?

Kind Regards,
Antara

--
Junior research fellow(project)
Systems biology group
CSIR-Institute of Genomics & Integrative Biology
South Campus
New Delhi -  110020
M : +91-9717970040
--



On Sun, May 15, 2016 at 10:51 AM, <
gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote:

> Send gromacs.org_gmx-users mailing list submissions to
> gromacs.org_gmx-users@maillist.sys.kth.se
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> or, via email, send a message with subject or body 'help' to
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>
> 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. COM-Pull along a direction (Pengzhi Zhang)
>2. Re: error in running mdrun of membrane protein in a mixed
>   bilayer with MARTINI MODEL (Justin Lemkul)
>3. Umbrella Sampling - choice of pull-coord?-dim (Lukas Zimmermann)
>4. PCA and FEL (sun)
>5. Re: PCA and FEL (Tsjerk Wassenaar)
>
>
> --
>
> Message: 1
> Date: Sat, 14 May 2016 14:58:37 -0500
> From: Pengzhi Zhang 
> To: 
> Subject: [gmx-users] COM-Pull along a direction
> Message-ID: <5737836d.8010...@central.uh.edu>
> Content-Type: text/plain; charset="utf-8"; format=flowed
>
> Dear Gromacs users,
>
> I am trying to pull an ion out of a protein using Gromacs/5.0.4. I pull
> the ion along specific pre-determined paths.
>
>  From my understanding, pulling along a direction _V guarantees that the
> dumb bead would move only at direction _V. The position of the dumb bead
> is simply: _r(t) = _r(0) + _V*speed*time (_ means vector). And if the
> spring constant is sufficiently large, the pulled atom (a single ion)
> would also follow the dumb bead (with fluctuations). However, I found
> that no matter how large the spring constant is (I vary it from 100 to
> 1,000,000 kJ/mol/nm**2), the pulled atom deviates from the direction _V
> in a certain amount of time (usually after the pulled bead unbinds),
> sometimes it even goes perpendicular to _V and moves out of the box,
> terminating the simulation.
>
> Does the direction _V (pull-coord1-vec) mean the direction of
> instantaneous pull force or the direction of the path that the dumb bead
> follows?
>
> Thank you very much in advance!
>
>
> Here is the pull part of my mdp file.
> ; COM PULLING
> ; Pull type: no, umbrella, constraint or constant-force
> pull= umbrella
> pull-geometry= direction
> pull-ngroups  = 2
> pull-ncoords  = 1
> pull-group1-name  = binding_site_atoms
> pull-group2-name  = pull_ion   ; pull group
> pull-start= yes
> pull-coord1-vec  = -0.07 -0.04 0.99
> pull-coord1-groups= 1 2
> pull_coord1_rate= 0.001; nm/ps
> pull-coord1-k = 1   ; kJ/mol/nm^2
> pull-nstxout   = 10 ; 0.02 ps
> pull-nstfout= 10
> pull-print-reference= yes
>
>
> Sincerely,
> Pengzhi
>
>
> --
>
> Message: 2
> Date: Sat, 14 May 2016 18:33:08 -0400
> From: Justin Lemkul 
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] error in running mdrun of membrane protein in
> a mixed bilayer with MARTINI MODEL
> Message-ID: <5b732333-0517-e66f-2e4b-7a9cf337e...@vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 5/14/16 2:34 PM, Mark Abraham wrote:
> > Hi,
> >
> > Please keep the discussion on the mailing list, so others can help and
> > learn.
> >
> >> Antara said:
> >> I have pasted the mdrun command i used to run it in parallel with the
> > number of processors i used which was 16. The command is :
> >>
> >>
> >> /app/setups/gromacs-5.1.1/build/bin -deffnm MD -pin on -rdd 1.8
> >
> > That still isn't a command you've copied and pasted from a terminal or a
> > script. You needed a call that might include mpirun -np 16 gmx_mpi mdrun,
> > etc.
> >
> >> In the pbs script, i used 16 in the number of processors option.
> >
> > What happens when you run on one rank?
> >
> >> For the production tpr, i used the gro file from the last equilibration
> > step(step6.6) The command used was :
> >>
> >> gmx grompp -c step6.6equilibration.gro -p system.top -n new_index.ndx -f
> > MD.mdp -o MD.tpr
> >
> > That looks like it could be reasonable, but as with any equilibration you
> > need to look at observables to judge that it's equilibrated. Their
> builder
> > should provide reasonable defaults, but you 

Re: [gmx-users] PCA and FEL

[sun]

Allright Sir
Thank you very much for clearing the point. 
With Regards
Suniba

Sent from my iPhone

> On 15-May-2016, at 12:14 pm, Tsjerk Wassenaar  wrote:
> 
> Hi Suniba,
> 
> No, you will get the stability of configuration in the order parameters you
> choose. But you don't know how much conformational freedom you have at each
> point. Low RMSD will mean stable, but a fixed point at high RMSD does not.
> Also note that the Rg is sort of part of the RMSD, which can be written as
> Rg(A)+Rg(B)-2S(A,B), where S is the similarity. So these order parameters
> will be correlated.
> 
> Cheers,
> 
> Tsjerk
> 
>> On Sun, May 15, 2016 at 8:13 AM, sun  wrote:
>> 
>> Thank you very much Sir. I get you. Is it good enough to probe the
>> stability of complex by projecting any two variables with free energy? like
>> RMSD and Rg?
>> 
>> 
>> Sent from my iPhone
>> 
>>> On 15-May-2016, at 10:51 am, Tsjerk Wassenaar  wrote:
>>> 
>>> Hi Suniba,
>>> 
>>> No, with gmx anaeig you can select -2d, which does a 2D projection onto
>> the
>>> selected eigenvectors. Alternatively, you can combine any two projections
>>> onto eigenvectors, which you get using the option -proj. The quickest way
>>> to do that is something like:
>>> 
>>> paste <(grep -v '^[@#]'  proj1.xvg) <(proj2.xvg) | awk '{print $2, $4}' >
>>> combined.xvg
>>> 
>>> You will loose the labels, but that should be fine.
>>> 
>>> You can combine other variables in a similar manner.
>>> 
>>> Hope it helps,
>>> 
>>> Tsjerk
>>> 
 On Sun, May 15, 2016 at 5:33 AM, sun  wrote:
 
 Hello everyone
 I am using Gromacs 5.0 for protein-ligand MD. I want to do FEL analysis
 for the stability of my pro-lig complex.   In a 2015 paper, The group
 calculated two principal component, PC1 and PC2 and then prepared an.xvg
 file to be used as input for g_sham. My question is, when we use
>> g_anaeig;
 we get eigenvec.xvg. from -comp flag. Now how shall one select two
 principal components from that data? I am sorry if my question is wrong
>> but
 please help me.
 
 My second question is, can we use any two parameters like rmsd and Rg
>> for
 input in g_sham to probe the stability of complex? Is that valid?
 
 With Regards
 Suniba
 
 Sent from my iPhone
 --
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 http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
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>>> 
>>> 
>>> 
>>> --
>>> Tsjerk A. Wassenaar, Ph.D.
>>> --
>>> Gromacs Users mailing list
>>> 
>>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
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> 
> 
> 
> -- 
> Tsjerk A. Wassenaar, Ph.D.
> -- 
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Re: [gmx-users] PCA and FEL

[Tsjerk Wassenaar]

Hi Suniba,

No, you will get the stability of configuration in the order parameters you
choose. But you don't know how much conformational freedom you have at each
point. Low RMSD will mean stable, but a fixed point at high RMSD does not.
Also note that the Rg is sort of part of the RMSD, which can be written as
Rg(A)+Rg(B)-2S(A,B), where S is the similarity. So these order parameters
will be correlated.

Cheers,

Tsjerk

On Sun, May 15, 2016 at 8:13 AM, sun  wrote:

> Thank you very much Sir. I get you. Is it good enough to probe the
> stability of complex by projecting any two variables with free energy? like
> RMSD and Rg?
>
>
> Sent from my iPhone
>
> > On 15-May-2016, at 10:51 am, Tsjerk Wassenaar  wrote:
> >
> > Hi Suniba,
> >
> > No, with gmx anaeig you can select -2d, which does a 2D projection onto
> the
> > selected eigenvectors. Alternatively, you can combine any two projections
> > onto eigenvectors, which you get using the option -proj. The quickest way
> > to do that is something like:
> >
> > paste <(grep -v '^[@#]'  proj1.xvg) <(proj2.xvg) | awk '{print $2, $4}' >
> > combined.xvg
> >
> > You will loose the labels, but that should be fine.
> >
> > You can combine other variables in a similar manner.
> >
> > Hope it helps,
> >
> > Tsjerk
> >
> >> On Sun, May 15, 2016 at 5:33 AM, sun  wrote:
> >>
> >> Hello everyone
> >> I am using Gromacs 5.0 for protein-ligand MD. I want to do FEL analysis
> >> for the stability of my pro-lig complex.   In a 2015 paper, The group
> >> calculated two principal component, PC1 and PC2 and then prepared an.xvg
> >> file to be used as input for g_sham. My question is, when we use
> g_anaeig;
> >> we get eigenvec.xvg. from -comp flag. Now how shall one select two
> >> principal components from that data? I am sorry if my question is wrong
> but
> >> please help me.
> >>
> >> My second question is, can we use any two parameters like rmsd and Rg
> for
> >> input in g_sham to probe the stability of complex? Is that valid?
> >>
> >> With Regards
> >> Suniba
> >>
> >> Sent from my iPhone
> >> --
> >> 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-requ...@gromacs.org.
> >
> >
> >
> > --
> > Tsjerk A. Wassenaar, Ph.D.
> > --
> > Gromacs Users mailing list
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-- 
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Re: [gmx-users] PCA and FEL

[sun]

Thank you very much Sir. I get you. Is it good enough to probe the stability of 
complex by projecting any two variables with free energy? like RMSD and Rg? 


Sent from my iPhone

> On 15-May-2016, at 10:51 am, Tsjerk Wassenaar  wrote:
> 
> Hi Suniba,
> 
> No, with gmx anaeig you can select -2d, which does a 2D projection onto the
> selected eigenvectors. Alternatively, you can combine any two projections
> onto eigenvectors, which you get using the option -proj. The quickest way
> to do that is something like:
> 
> paste <(grep -v '^[@#]'  proj1.xvg) <(proj2.xvg) | awk '{print $2, $4}' >
> combined.xvg
> 
> You will loose the labels, but that should be fine.
> 
> You can combine other variables in a similar manner.
> 
> Hope it helps,
> 
> Tsjerk
> 
>> On Sun, May 15, 2016 at 5:33 AM, sun  wrote:
>> 
>> Hello everyone
>> I am using Gromacs 5.0 for protein-ligand MD. I want to do FEL analysis
>> for the stability of my pro-lig complex.   In a 2015 paper, The group
>> calculated two principal component, PC1 and PC2 and then prepared an.xvg
>> file to be used as input for g_sham. My question is, when we use g_anaeig;
>> we get eigenvec.xvg. from -comp flag. Now how shall one select two
>> principal components from that data? I am sorry if my question is wrong but
>> please help me.
>> 
>> My second question is, can we use any two parameters like rmsd and Rg for
>> input in g_sham to probe the stability of complex? Is that valid?
>> 
>> With Regards
>> Suniba
>> 
>> Sent from my iPhone
>> --
>> 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-requ...@gromacs.org.
> 
> 
> 
> -- 
> Tsjerk A. Wassenaar, Ph.D.
> -- 
> 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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