Re: [gmx-users] problem with MPI,thread and number of CPU

[Mark Abraham]

Hi,

On Mon, May 16, 2016 at 9:13 PM  wrote:

>
>
> 
> p { margin-bottom: 0.1in; line-height: 120%; }a:link {  }
>
>
> Dear Gromacs users
>
>
> During simulating DPPC membrane I confront with several Problems. I
> intend to express them here and I really appreciate it if you help me.
> Briefly I started to simulate a DPPC containing 2000 W and 128 DPPC
> molecules. the trend ( I mean the way it increase or decrease) of
> Pressure xx is important to me. as one can expect, due to the size of my
> system ( number of atom) the result is so erratic  ( about 200bar).
> so I enlarge the system in X-direction considering consistent trend for
> both system. so I replicated system in X-direction, minimized it and do
> an NPT on it.
>

A common mistake here is to concatenate boxes without leaving a suitable
spacing between them, because atoms whose centers are close to the old
edges of the box can now be too close to their new neighbours.


> during NPT, my working job blew up with this error :
>
>
> An atom moved too far between two domain decomposition steps
>
>
> does this error relate to the number of cpu-cores, because when I
> decrease number of the cores from 16 to 8 using -nb 8, I dont see
> this error again, but there is no progress in the number of steps !!!
>

Different parallelism leads to different forces, and (in this case)
different ways for the simulation to blow up, particularly if my guess is
correct.


> also I have question about MPI. In my laptop when I simulate a box
> ( 128
> DPPC with 2000 W), the system runs with :
>
>
> Using 1 MPI thread
>
> Using 4 OpenMP threads
>
>
> when I do the same, in High performance Computer of the
> university, Its
> output is totally different which also uses automatically :
>
>
> Using 24 MPI threads
>
> Using 1 OpenMP thread per tMPI thread
>
>
> but when I used -ntmpi 1 to change MPI threads to 1, it gave the
> same
> answer as my laptop. so what is the optimum number of -ntmpi and -nt ?! I
> should notice that I now what is the meaning of MPI and thread, but
> dont now what is the optimum number 
>

It varies. mdrun has some heuristics that consider the kind of processor,
the number of cores, the number of atoms, the presence of GPUs, the value
of environment variables like OMP_NUM_THREADS...

Mark


>
> best  regards
>
>
> Ali
>
>
> ==
>
>
> Ali khourshaei shargh (khourshaeisha...@mech.sharif.ir)
>
>
> Department of Mechanical Engineering
>
>
> Sharif University of Technology, Tehran, Iran
>
>
>
>
>
>
>
>
>
>
>
>
>
> --
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[gmx-users] problem with MPI,thread and number of CPU

[khourshaeishargh]

p { margin-bottom: 0.1in; line-height: 120%; }a:link {  }


Dear Gromacs users


During simulating DPPC membrane I confront with several Problems. I
intend to express them here and I really appreciate it if you help me.
Briefly I started to simulate a DPPC containing 2000 W and 128 DPPC
molecules. the trend ( I mean the way it increase or decrease) of
Pressure xx is important to me. as one can expect, due to the size of my
system ( number of atom) the result is so erratic� ( about 200bar).
so I enlarge the system in X-direction considering consistent trend for
both system. so I replicated system in X-direction, minimized it and do
an NPT on it.


during NPT, my working job blew up with this error :


An atom moved too far between two domain decomposition steps


does this error relate to the number of cpu-cores, because when I
decrease number of the cores from 16 to 8 using -nb 8, I dont see
this error again, but there is no progress in the number of steps !!!


also I have question about MPI. In my laptop when I simulate a box ( 128
DPPC with 2000 W), the system runs with :


Using 1 MPI thread

Using 4 OpenMP threads


when I do the same, in High performance Computer of the university, Its
output is totally different which also uses automatically :


Using 24 MPI threads

Using 1 OpenMP thread per tMPI thread


but when I used -ntmpi 1 to change MPI threads to 1, it gave the same
answer as my laptop. so what is the optimum number of -ntmpi and -nt ?! I
should notice that I now what is the meaning of MPI and thread, but
dont now what is the optimum number 


best� regards


Ali


==


Ali khourshaei shargh (khourshaeisha...@mech.sharif.ir)


Department of Mechanical Engineering


Sharif University of Technology, Tehran, Iran




�




�

�

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[gmx-users] improper .gro file format generated by trjconv

[Esra Kaçar]

Dear gromacs users;

I am trying to perform micelle clustering analysis as described in gromcas
website:

   1. use trjconv
    -pbc
   cluster to obtain a single frame that has all of the lipids in the unit
   cell. This must be the first frame of your trajectory. A similar frame from
   some previous timepoint will not work.
   2. use grompp
    to make
   a new tpr file based on the frame that was output from the step above.
   3. use trjconv
    -pbc
   nojump to produce the desired trajectory using the newly produced tpr
   file.

Firstly I am trying to use trjconv to have a .gro file, but the output of
first step gives me a .gro file in improper format, i.e.coordinates are not
written with required spaces between each other. Here is my command line:

gmx trjconv -f mytrajectory.xtc -o micelle.gro -s mytopology.tpr -e 0.001
-pbc cluster

And here is the micelle.gro file:

1CHOA   ROH1   2.7   8.2   7.7
1CHOA  R12   3.0   8.1   7.7
1CHOA  R23   3.2   8.1   7.8
1CHOA   RO24   3.2   7.8   7.7
1CHOA   RO35   3.4   7.8   7.9
1CHOA  R36   3.4   7.8   7.7
1CHOA  C17   3.6   7.5   7.7
1CHOA   OCO8   3.5   7.1   7.6

What can be the possible reason for this error and how can I fix it?

With regards,
Esra
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[gmx-users] tutor/speptide

[Alexander Alexander]

Dear Gromacs user,

In below link where the S-peptide has been taught for the beginner, they
point out that the tutorial materials have been stored in the directory
"tutor/speptide", would you please let me know where I can find this
directory or have access to this directory?

http://manual.gromacs.org/archive/4.6.6/online/speptide.html

Thanks,
Cheers,
Alex
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Re: [gmx-users] tutor/speptide

[Justin Lemkul]

On 5/16/16 9:51 AM, Alexander Alexander wrote:

Dear Gromacs user,

In below link where the S-peptide has been taught for the beginner, they
point out that the tutorial materials have been stored in the directory
"tutor/speptide", would you please let me know where I can find this
directory or have access to this directory?

http://manual.gromacs.org/archive/4.6.6/online/speptide.html



Outdated documentation.  The "tutor" subdirectory was removed prior to version 
4.6 as it was generally not very useful and therefore undesirable to maintain. 
Comprehensive tutorials are linked on the GROMACS webpage.


-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

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Re: [gmx-users] Calculating Distance

[Justin Lemkul]

On 5/16/16 3:20 AM, Sanket Ghawali wrote:

Dear, gmx-users,

Hello everyone,
I'm simulating a peptide in an SDS micelle. The simulation was
performed for 100ns
When I visualize the trajectory in VMD, the peptide moves to the SDS
interface where initially it was placed in the center,  the results
are as expected. I would like to calculate the distance the peptide
has traveled or moved from the center to the interface


Any suggestions on how to go about doing this?



Calculating distances is what the gmx distance program is for.  Simply obtain 
the COM distance between the micelle and peptide (or any subset of atoms that 
makes sense).


-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

==
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Re: [gmx-users] simulation_time

[Justin Lemkul]

On 5/16/16 12:23 AM, Ms. Nikita Bora wrote:

 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??



Different force fields, different settings.

-Justin




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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--
==

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

==
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[gmx-users] heat of vaporization

[Saitama Lawliet]

Hi all

I am trying to calculate heat of vaporization of tri-ethyl phosphate (tep).
I took 500 tep molecules for MD simulation. After energy minimization and
NVT I performed NPT simulation for 10ns with usual PBC, dispersion
correction etc.
>From the final results using g_energy -nmol 500 I got the potential energy
of -155.406kj/mol.
The density  of the liquid tep was 1085.8kg/m3 which is very close to the
earlier MD reported data.
Then I took one single tep molecule in a box and perform the calculation
without using pbc and all cut-off to zero. The potential energy I got was
-692.13kj/mol.

Now as per defintion of HVap= U(gas)- U(liquid) +RT
 I am getting the value of Hvap of tep as: -534.25kj/mol whereas the
reported value is 77.69kj/mol. what is wrong I am unable to find out.
Any help to sort out this mistake will be highly appreciated.

warm regards

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

[Husen R]

Hi all,

After spending time for troubleshooting, I found that gromacs
checkpoint/restart feature is working well.

The failure occurred because I use root user to submit restart job (using
slurm resource manager). After switching to non root user, the restart
process is running.
The reason why I use root user is because I run this job in bash scripting
and execute it at designated time using Cron.
I know this is not the right place to talk about slurm.

Thank you for your reply !

Regards,

Husen

On Sun, May 15, 2016 at 8:20 PM,  wrote:

> 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 

Re: [gmx-users] Removing periodic boundary condition

[Tsjerk Wassenaar]

Hi Sanket,

Can you check the structure in the tpr file (editconf -f .tpr -o
.gro/.pdb)? If that is good, then -pbc nojump should work. For the second
pass, you shouldn't need -pbc mol then.

Cheers,

Tsjerk
On May 16, 2016 9:06 AM, "Sanket Ghawali"  wrote:

> Dear, gmx-users,
>
> Hello everyone,
> I'm simulating a peptide in an SDS micelle. The simulation was
> performed for 100ns
> When I view the trajectory in VMD, a portion of the SDS micelle moves
> to the right and goes into the next box. Of course, because of
> periodic boundary conditions. I tried using trjconv to see if I could
> suppress the periodic boundary conditions for the purpose of
> visualization. I've used all the different -pbc options none of them
> helped.
>
> options i have used
>
> trjconv -f .trr -s .tpr -o nojump.trr -pbc nojump
>
> used the above created nojump.trr in the below command
>
> trjconv -f nojump.trr -s .tpr -n .ndx -o .trr -b 0 -e 10 -ur
> compact -pbc mol -center
>
> Selected Protein as centering group and system as output group
>
>
> Any suggestions on how to go about doing this?
>
> Thanks,
>
> Sanket
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Re: [gmx-users] Calculating Distance

[masoud keramati]

choose a atom, then calculate the transition vector of it with use of the
initial and final coordinate.


On Mon, May 16, 2016 at 11:50 AM, Sanket Ghawali 
wrote:

> Dear, gmx-users,
>
> Hello everyone,
> I'm simulating a peptide in an SDS micelle. The simulation was
> performed for 100ns
> When I visualize the trajectory in VMD, the peptide moves to the SDS
> interface where initially it was placed in the center,  the results
> are as expected. I would like to calculate the distance the peptide
> has traveled or moved from the center to the interface
>
>
> Any suggestions on how to go about doing this?
>
> Thanks,
>
> Sanket
> --
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[gmx-users] Calculating Distance

[Sanket Ghawali]

Dear, gmx-users,

Hello everyone,
I'm simulating a peptide in an SDS micelle. The simulation was
performed for 100ns
When I visualize the trajectory in VMD, the peptide moves to the SDS
interface where initially it was placed in the center,  the results
are as expected. I would like to calculate the distance the peptide
has traveled or moved from the center to the interface


Any suggestions on how to go about doing this?

Thanks,

Sanket
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[gmx-users] Removing periodic boundary condition

[Sanket Ghawali]

Dear, gmx-users,

Hello everyone,
I'm simulating a peptide in an SDS micelle. The simulation was
performed for 100ns
When I view the trajectory in VMD, a portion of the SDS micelle moves
to the right and goes into the next box. Of course, because of
periodic boundary conditions. I tried using trjconv to see if I could
suppress the periodic boundary conditions for the purpose of
visualization. I've used all the different -pbc options none of them
helped.

options i have used

trjconv -f .trr -s .tpr -o nojump.trr -pbc nojump

used the above created nojump.trr in the below command

trjconv -f nojump.trr -s .tpr -n .ndx -o .trr -b 0 -e 10 -ur
compact -pbc mol -center

Selected Protein as centering group and system as output group


Any suggestions on how to go about doing this?

Thanks,

Sanket
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