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Today's Topics:
1. Re: simulation termination problem (Prabir Khatua)
2. Re: wham analysis (Justin Lemkul)
3. Re: Domain decomposition error while running coarse grained
simulations on cluster (Justin Lemkul)
4. Re: mdrun error (Justin Lemkul)
5. regarding changing the scale from ps to ns (sudha bhagwati)
----------------------------------------------------------------------
Message: 1
Date: Sun, 1 Sep 2019 12:10:04 -0500
From: Prabir Khatua <prabir07c...@gmail.com>
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] simulation termination problem
Message-ID:
<
caobzxoogmnzmky8ddreyhfh7cjm9ycppo3fg6dmoe5fn-mg...@mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"
Thanks Justin. The problem has been fixed.
On Fri, Aug 30, 2019 at 7:31 AM Justin Lemkul <jalem...@vt.edu> wrote:
On 8/29/19 12:31 PM, Prabir Khatua wrote:
Hello Gromacs users,
I am trying to simulate a system of atom size 3,58,973 in gromacs
5.1.5.
However, my simulation is being terminated in between with the
following
error.
File input/output error:
Cannot rename checkpoint file; maybe you are out of disk space?
For more information and tips for troubleshooting, please check the
GROMACS
website at http://www.gromacs.org/Documentation/Errors
I did not find any solution with respect to the error I was having in
the
mentioned website. What I found was related to memory issue. I do not
know
whether this is the same issue.
The issue is not related to memory, it is (potentially) related to disk
space. Do you have enough space on the filesystem to write output files?
This can also happen sometimes when the filesystem blips. There's not
much you can do about that except complain to your sysadmin about
integrity of the filesystem.
-Justin
Please note that I was successfully able to run another simulation of a
system having relatively less number of atoms with same script. The run
command that I used for the simulation was
mpirun -np 48 gmx_mpi mdrun -ntomp 1 -deffnm npt
I ran both the simulations on two nodes having 24 cpu cores in each one
of
the nodes.
I am also not able to figure out one issue. The log file of the system
where the simulation was successfully completed showed
Running on 2 nodes with total 48 cores, 48 logical cores, 0 compatible
GPUs
Cores per node: 24
Logical cores per node: 24
Compatible GPUs per node: 0
However, in the unsuccessful case, the log file showed
Running on 1 node with total 24 cores, 24 logical cores
Thus, it looks like the simulation was running on single node although
I
asked it to run on two nodes. I have no idea how to fix this issue.
Please
help me fix this issue or what I am doing wrong.
Thanks in advance,
Prabir
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
==================================================
--
Gromacs Users mailing list
* Please search the archive at
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* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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--
*Prabir Khatua*
*Postdoctoral Research Associate*
*Department of Chemistry & Biochemistry*
*University of Oklahoma*
*Norman, Oklahoma 73019*
*U. S. A.*
------------------------------
Message: 2
Date: Sun, 1 Sep 2019 13:21:23 -0400
From: Justin Lemkul <jalem...@vt.edu>
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] wham analysis
Message-ID: <65191dc8-43fd-bc2f-6b9a-20903052d...@vt.edu>
Content-Type: text/plain; charset=utf-8; format=flowed
On 9/1/19 5:35 AM, Negar Parvizi wrote:
Dear all,
I used Justin tutorial(Tutorial 3: Umbrella Sampling: GROMACS Tutorial )
for my file which is protein-ligand complex.
The pulling force was in Y direction. when Umbrella sampling finished,
"Wham" couldn't analysis the data because wham is in z direction.what
should I do now for wham analysis? how can I change it to Y direction?
I sent message in gromacs comunity , what Justin said:
"WHAM does not presuppose the axis or vector; it does what you tell it.
If you're referring to the x-axis label in the PMF profile being "z," that
is just a generic (and perhaps imprecise) label that should be changed to
the Greek character xi, per conventional notation."
I didn't understand it.
I made a guess based on minimal information. You asserted that you
pulled along y but WHAM indicated the bias was along z. I know that the
default x-axis label in profile.xvg says "z" and it causes confusion. So
I provided the comment that I did.
However, it is clear from the gmx wham output below that you did *not*
apply a bias along y, as you stated:
File umbrella0.tpr, 1 coordinates, geometry "distance", dimensions [N N
Y], (1 dimensions)
This means your reaction coordinate was the z-axis.
So I decided copy the error:
Here is the error:
Found 25 tpr and 25 pull force files in tpr-files.dat and
pullf-files.dat, respectively
Reading 12 tpr and pullf files
Automatic determination of boundaries...
Reading file umbrella0.tpr, VERSION 5.1.4 (single precision)
File umbrella0.tpr, 1 coordinates, geometry "distance", dimensions [N N
Y], (1 dimensions)
Pull group coordinates not expected in pullx files.
crd 0) k = 1000 position = 0.840198
Use option -v to see this output for all input tpr files
Reading pull force file with pull geometry distance and 1 pull
dimensions
Expecting these columns in pull file:
0 reference columns for each individual pull coordinate
1 data columns for each pull coordinate
With 1 pull groups, expect 2 columns (including the time column)
Reading file umbrella71.tpr, VERSION 5.1.4 (single precision)
Reading file umbrella98.tpr, VERSION 5.1.4 (single precision)
Reading file umbrella111.tpr, VERSION 5.1.4 (single precision)
Reading file umbrella119.tpr, VERSION 5.1.4 (single precision)
Reading file umbrella139.tpr, VERSION 5.1.4 (single precision)
Reading file umbrella146.tpr, VERSION 5.1.4 (single precision)
Reading file umbrella157.tpr, VERSION 5.1.4 (single precision)
Reading file umbrella180.tpr, VERSION 5.1.4 (single precision)
Reading file umbrella202.tpr, VERSION 5.1.4 (single precision)
What happens next? Nothing here says "error," however it looks like your
input files are of an unexpected format. Perhaps you've switched
pullx.xvg and pullf.xvg. As someone else suggested, you can use
pullf.xvg files to get the PMF profile and avoid the issue entirely.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
==================================================
------------------------------
Message: 3
Date: Sun, 1 Sep 2019 13:22:15 -0400
From: Justin Lemkul <jalem...@vt.edu>
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Domain decomposition error while running
coarse grained simulations on cluster
Message-ID: <71840e02-8747-38b0-d2a0-39da5adbb...@vt.edu>
Content-Type: text/plain; charset=utf-8; format=flowed
On 9/1/19 5:44 AM, Avijeet Kulshrestha wrote:
Hi all,
I am running martini coarse-grained simulation with 15 fs of time step in
gromacs 2018.6. I have 25859 number of atoms and my box size is:
12.00000 14.00000 18.00000
Where I have Protein, membrane (DPPC) and ions.
I have minimized energy with 16 processor and -rdd option as 2.5. It
worked
fine but later in NVT simulation, this started giving errors.
*I am getting the following error without -rdd option when I used 1 node
and 8 processor per node:*
Fatal error:
There is no domain decomposition for 8 ranks that is compatible with the
given
box and a minimum cell size of 7.69783 nm
This minimum cell size is significantly larger than a normal simulation
would require. Do you have restraints or other non-standard interactions
defined? The .log file snippet that describes the DD setup would be
useful for tracking the issue down.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
==================================================
------------------------------
Message: 4
Date: Sun, 1 Sep 2019 13:23:48 -0400
From: Justin Lemkul <jalem...@vt.edu>
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] mdrun error
Message-ID: <a3299ee2-b645-a330-65f8-3bd18d65a...@vt.edu>
Content-Type: text/plain; charset=utf-8; format=flowed
On 9/1/19 7:02 AM, m g wrote:
Dear Justin,
There are many other people on this list, and I don't always have answers
:)
I'm simulating a system with "wall" for z direction, but I gave this
error in minimization step "software inconsistency error: lost particles
while sorting",.Would you please help me? I used the following?parameter:
What GROMACS version are you using? CPU or GPU? Does the simulation work
without the walls? You need to provide a lot more diagnostic
information. This is a cryptic error that suggests something very
fundamental is wrong. That also makes it very hard to diagnose.
If you're not using the latest version of GROMACS, start there. I recall
some bug fixes that may be relevant. If the error is reproducible in
2019.3, please post a more complete description of what you're doing.
-Justin
integrator? ??? =steep
emtol?????? ?? ?????= 100.0emstep????????????? = 0.01nsteps???????????
??? = 5000nstlist?????????? ??? = 1cutoff-scheme?????? =
Verletns_type?????????? ??? = gridrlist?????? ?? ?????= 1.2? ??coulombtype
?? ?????= PMErcoulomb??? ?? ?????= 1.2vdwtype???????????? =
cutoffvdw-modifier??????? = force-switchrvdw-switch???????? =
1.0rvdw??????? ? ??????= 1.2????????? ??DispCorr??????????? = nopbc ?
??????????????=xy? ? ? ? ? ? ? ? ? ??nwall?????????????? =
2wall_type?????????? = 10-4wall_r_linpot?????? = 1wall_atomtype?????? = ca?
cawall_density??????? = 60? 60wall_ewald_zfac???? = 3ewald-geometry????? =
3dc
Thanks,Ganj
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
==================================================
------------------------------
Message: 5
Date: Mon, 2 Sep 2019 12:23:25 +0530
From: sudha bhagwati <sudhabhagw...@gmail.com>
To: gmx-us...@gromacs.org
Subject: [gmx-users] regarding changing the scale from ps to ns
Message-ID:
<CAAjYSb-58-5qEeM+Rq-Yv3yTApA8cb1ktL_DP74n8MoK3j=
3...@mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"
Dear gmx users,
I am using the GROAMCS 5.1.4 version.
----------------------------------------------------------------------------------------------------------------------------------------
Running the commands below:
*gmx gyrate -s md_0_20.tpr -f md_0_20_noPBC.xtc -o gyrate.xvg -tu ns*
*OR*
*gmx energy -f ie.edr -o interaction_energy.xvg -tu ns*
Error while executing commands:
*Error in user input:*
*Invalid command-line options Unknown command-line option -tu*
----------------------------------------------------------------------------------------------------------------------------------------
-tu flag is not working for commands showed above. I want to generate my
plots for nanosecond scale using xmgrace. Could you please help me out with
this issue. I'd be really grateful to you.
Thank you.
--
Thanks & regards
~
Sudha Bhagwati
------------------------------
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End of gromacs.org_gmx-users Digest, Vol 185, Issue 3
*****************************************************
