[gmx-users] Error in gromacs-5.1 installation

[Venkat Reddy]

Dear all,
We have a GPU workstation populated with four C2075 cards. I have
previously installed and used Gromacs-5.04 without any problem. But when I
tried to install Gromacs-5.1 version, "make" command is terminating with
the following error:

/home/dynamix/Downloads/gromacs-5.1/src/gromacs/gmxlib/gpu_utils/
gpu_utils.cu(360): error: identifier
"NVML_RESTRICTED_API_SET_APPLICATION_CLOCKS" is undefined

/home/dynamix/Downloads/gromacs-5.1/src/gromacs/gmxlib/gpu_utils/
gpu_utils.cu(360): error: identifier "nvmlDeviceGetAPIRestriction" is
undefined

2 errors detected in the compilation of
"/tmp/tmpxft_2f84_-12_gpu_utils.compute_35.cpp1.ii".
CMake Error at libgromacs_generated_gpu_utils.cu.o.cmake:266 (message):
  Error generating file

/home/dynamix/Downloads/gromacs-5.1/build/src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/gpu_utils/./libgromacs_generated_gpu_utils.cu.o

make[2]: ***
[src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/gpu_utils/libgromacs_generated_gpu_utils.cu.o]
Error 1
make[2]: *** Waiting for unfinished jobs
make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
make: *** [all] Error 2

Thanks for your concern

-- 
With Best Wishes
Venkat
-- 
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.

[gmx-users] Hybrid acceleration with "well-tempered parallel tempering metadynamics"

[Francesco Carbone]

good afternoon all,
I'm having problems in running a "well-tempered parallel tempering
metadynamics" with gromacs 5.

The problem is that I don't understand how to set -multi based on the cpu I
have (the cluster has both 12 and 16 cpu x node).

If I want to run 10 replicas spread over 160 cores I set:

mpirun -np 160 mdrun_mpi -ntomp 16 -v -s input.tpr -plumed -multi 10
-replex 500 -o wt_20t1 2>gmx_error.err

This should start 10 MPI thread with 16 OpenMP each.
Instead I get 16 MPI with 16 OpenMPI and in the log I read:

"Number of hardware threads detected (16) does not match the number
reported by OpenMP (1).
Consider setting the launch configuration manually!
Using 16 MPI processes
Using 16 OpenMP threads per MPI process
WARNING: Oversubscribing the available 16 logical CPU cores with 256
threads.
 This will cause considerable performance loss!
Non-default thread affinity set probably by the OpenMP library,
disabling internal thread affinity"

In the "multi-level parallelization" section of the documentation (
http://www.gromacs.org/Documentation/Acceleration_and_parallelization#Running_simulations)
I found that I should use "mpirun -np M mdrun_mpi -ntomp N" with M number
of total cores and N number of OpenMP.
Because I have 16 cores x node, setting -ntomp to 16 is correct as 16x1
(OpenMPx MPI) gives 16, which is a multiple of the cores I have per node.

I tried setting export "OMP_NUM_THREADS=16" and then -ntomp
$OMP_NUM_THREADS, but nothing changed.

I also tried to let "gerun" handle all the setting and using OpenMP
mutithreading only (gerun mdrun_mpi -v -s input.tpr -plumed -multi 10
-replex 500 -o wt_20t1 2>gmx_error.err).
In this case after the same messages (Number of hardware threads detected
(16) does not match the number reported by OpenMP (1). Consider setting the
launch configuration manually!) I get 1 MPI and 16 OpenMPI, but in this
case the predicted running time is huge compare to when I have "performance
loss!" (from 9th October as predicted end to 21st of January for a 50ns
with ~190.000 atoms ).

How is it possible? how does it work?

this is the script I'm using (I tried several combination of mdrun_mpi):

#!/bin/bash -l

#$ -S /bin/bash
#$ -l h_rt=0:15:0
#$ -l mem=1G
#$ -l tmpfs=15G
#$ -N ciao
#$ -pe qlc 160
#$ -wd /home/ucbtca4/Scratch/metadynamics/ciao

module load gcc-libs/4.9.2
module load compilers/intel/2015/update2
module load mpi/intel/2015/update3/intel
module load openblas/0.2.14/intel-2015-update2
module load plumed/2.1.2/intel-2015-update2
module load gromacs/5.0.4/plumed/intel-2015-update2

export OMP_NUM_THREADS=16
export MPIRUN="/shared/ucl/apps/intel/2015/impi/5.0.3.048/intel64/bin/mpirun
"

$MPIRUN -np 160 mdrun_mpi -ntomp $OMP_NUM_THREADS -v -s input.tpr -plumed
-multi 10 -replex 500 -o wt_20t1 2>gmx_error.err

#gerun mdrun_mpi -v -s input.tpr -plumed -multi 10 -replex 500 -o wt_20t1
2>gmx_error.err
#gerun mdrun_mpi -ntomp $OMP_NUM_THREADS -v -s input.tpr -plumed -multi 10
-replex 500 -o wt_20t1 2>gmx_error.err
#gerun mdrun_mpi -v -s input.tpr -plumed -multi 10 -replex 500 -o wt_20t1
2>gmx_error.err
#mpirun -np 100 mdrun_mpi -ntomp 10 -v -s input.tpr -plumed -multi 10
-replex 500 -o wt_20t1 2>gmx_error.err
#mpirun -np 160 mdrun_mpi -ntomp 16 -v -s input.tpr -plumed -multi 10
-replex 500 -o wt_20t1 2>gmx_error.err

If I have gpus I set -np to the number of gpus and everything woks like a
charm, but I don't understand how to run it with cpus only.

thank you for your time,

Regards,

Francesco
-- 
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.

[gmx-users] Free energy in octanol and water

[Gmx QA]

Hi gmx-users

I am trying to calculate the free energy of solvation for a drug-molecule
in octanol and water.

I am comparing two situations:

A: Two systems, one with the drug in water only, and one with the drug in
pure octanol.

B: drug in water only (same as in A), and then one box where I have added
20% water to my octanol system (since mixtures of octanol and water
typically contains some water in the octanol phase).

Then I run a series of free energy calculations per Justin's tutorial, 48
lambda points in total.
For system A I get a Delta-G for pure water of 39.07 kJ/mol, and 92.81
kJ/mol in pure octanol.

For system B, the Delta-G for pure water is the same, but for the
octanol-box with 20% water the Delta-G is 95.99 kJ/mol.

All of these results are obtained using gmx bar in gromacs 5.0.4.

My main concern is that the Delta-G is higher in the water/octanol mixture
than in pure octanol, but I would have expected the reverse to be the case?

Is there something wrong with my protocol? The forcefield is
GAFF/amber99sb,and all production runs are 10 ns in length.

Best
/PK

I have uploaded copies of all input-files here:

https://dl.dropboxusercontent.com/u/66785227/md.mdp
https://dl.dropboxusercontent.com/u/66785227/npt.gro
https://dl.dropboxusercontent.com/u/66785227/octanol_GMX.itp
https://dl.dropboxusercontent.com/u/66785227/API_gmx.itp
https://dl.dropboxusercontent.com/u/66785227/topol.top
-- 
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.

Re: [gmx-users] g_covar error in Gromacs 5

[Justin Lemkul]

On 9/29/15 1:00 PM, Rebeca García Fandiño wrote:

Hi,
I am trying to use g_covar like this:

echo 2 2 | g_covar
-s prod_clus_1_exp.tpr -f prod_clus_exp_fit.xtc -n index_noH_exp.ndx -o
eigenval_300K_exp.xvg -v eigenvect_300K_exp.trr

In Gromacs 5.0.4 I get an error:

(...)

Choose a group for the least squares fit
Group 0 ( System) has  4437 elements
Group 1 (  Other) has   147 elements
Group 2 (MOL) has   147 elements
Select a group: 2
Selected 2: 'MOL'

Choose a group for the covariance analysis
Group 0 ( System) has  4437 elements
Group 1 (  Other) has   147 elements
Group 2 (MOL) has   147 elements
Select a group: 2
Selected 2: 'MOL'

Note: the fit and analysis group are identical,
   while the fit is mass weighted and the analysis is not.
   Making the fit non mass weighted.

Calculating the average structure ...
Reading frames from gro file 'frame t= 18.000', 4437 atoms.
Last frame  0 time   18.000

Back Off! I just backed up average.pdb to ./#average.pdb.4#
Constructing covariance matrix (441x441) ...
Reading frames from gro file 'frame t= 18.000', 4437 atoms.
Last frame  0 time   18.000
Read 1 frames

Trace of the covariance matrix: 0 (nm^2)

Diagonalizing ...

Sum of the eigenvalues: 0 (nm^2)
Violación de segmento


That
  means "Segmentation fault". The most strange is that using Gromacs
4.6.2 this error does not appear, and the command executes properly.
Could it be maybe a bug in Gromacs 5?



Yes, one that was fixed after 5.0.4.  When encountering potential bugs, always 
try upgrading to the latest version in your series (at least 5.0.6, if not 5.1) 
and try again.


-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.

[gmx-users] g_covar error in Gromacs 5

[Rebeca García Fandiño]

Hi,
I am trying to use g_covar like this:

echo 2 2 | g_covar 
-s prod_clus_1_exp.tpr -f prod_clus_exp_fit.xtc -n index_noH_exp.ndx -o 
eigenval_300K_exp.xvg -v eigenvect_300K_exp.trr 

In Gromacs 5.0.4 I get an error:

(...)

Choose a group for the least squares fit
Group 0 ( System) has  4437 elements
Group 1 (  Other) has   147 elements
Group 2 (MOL) has   147 elements
Select a group: 2
Selected 2: 'MOL'

Choose a group for the covariance analysis
Group 0 ( System) has  4437 elements
Group 1 (  Other) has   147 elements
Group 2 (MOL) has   147 elements
Select a group: 2
Selected 2: 'MOL'

Note: the fit and analysis group are identical,
  while the fit is mass weighted and the analysis is not.
  Making the fit non mass weighted.

Calculating the average structure ...
Reading frames from gro file 'frame t= 18.000', 4437 atoms.
Last frame  0 time   18.000

Back Off! I just backed up average.pdb to ./#average.pdb.4#
Constructing covariance matrix (441x441) ...
Reading frames from gro file 'frame t= 18.000', 4437 atoms.
Last frame  0 time   18.000
Read 1 frames

Trace of the covariance matrix: 0 (nm^2)

Diagonalizing ...

Sum of the eigenvalues: 0 (nm^2)
Violación de segmento


That
 means "Segmentation fault". The most strange is that using Gromacs 
4.6.2 this error does not appear, and the command executes properly. 
Could it be maybe a bug in Gromacs 5?

Thanks a lot for your help in advance.

Dr. Rebeca Garcia
Santiago de Compostela University (Spain)
  
-- 
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.

Re: [gmx-users] Pausing and resuming mdrun

[Andrew DeYoung]

Szilard,

Thanks for your time; it is really helpful.

Just in case people are reading this thread in the future, I want to point
out a mistake I made in my original message.  I said that using the signal
"-SIGSTP" was an alternative to -SIGSTOP.  It is actually "-SIGTSTP", not
"-SIGSTP".  -SIGTSTP is short for "_t_erminal stop," as this reference
page explains:

http://www.ucs.cam.ac.uk/docs/course-notes/unix-courses/Building/files/signals.pdf

Thanks again,

Andrew

-- 
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.

[gmx-users] Gromacs GPU got hang

[M Teguh Satria]

Hi All,

I am new in using Gromacs. I have a small HPC cluster and one of the nodes
has a Tesla K40 GPU. Now I have problem when trying to run a Gromacs GPU
job in that GPU node. It seems my job got hang after several hours running,
the gromacs log was stopped being updated and through nvidia-smi I saw the
GPU process became 0% GPU Util.

Any of you experiencing similar problem ? Is there any way to
troubleshoot/debug to see the cause ? Because I didn't get any warning or
error message.

Thanks in advance.

-- 
---
Regards,
Teguh
-- 
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.

Re: [gmx-users] Barostat Selection

[Parker de Waal]

Thank you for the prompt response Justin.

I was unaware that the relaxation time had no effect on simulation performance. 
Would you expect a difference between tau_p = 1.0 and 5.0 for production runs 
using Parrinello-Rahman?

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
Lemkul
Sent: Tuesday, September 29, 2015 9:00 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Barostat Selection



On 9/29/15 8:57 PM, Parker de Waal wrote:
> Hi everyone,
>
> I recently got into an interesting discussion regarding barostat selection 
> for NPT equilibration and later NPT production runs and was wondering what 
> the community thought on this issue.
>
> Specifically, for the initial NPT equilibrium, would it be acceptable 
> to use the berendsen barostat (tau_p = 1.0 ) and then later switch to 
> the Parrinello-Rahman barostat (tau_p = 5) for production, or would it 
> be best to stick with berendsen (keep tau_p = 1.0 or increase to 5.0 
> to increase ns/day?)
>

Barostat relaxation time should have no effect on performance.  The Berendsen 
weak coupling algorithms do not produce correct distributions and they should 
not be used for production simulations.  The algorithm is good for 
equilibration, but shouldn't be used for much else.

-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://secure-web.cisco.com/1ojLfbMlRYuefZ_1olbKjXPZp-h4B9atVOLOfNXQ7pczhcSv3VkmPlIgK3dmbOVGiGwMhCTCoZzv_jrbSSl3rJC35FBF34au6FR1lWqNwjUmLk1i-p8rHhXfjXJ8RiLsvoVuIxKtlum35oYjAa7eqmHBr2xfQ0a2cH-V3FI4YDUtttitIzcF1c177lFZnkxF9NEeJigdBkiDZVBjuINkIF7gVdNGETE1r8Eu6XjM24e4/http%3A%2F%2Fmackerell.umaryland.edu%2F%7Ejalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://secure-web.cisco.com/1MQxYm8ywdBbJUNmGzQcwWfpEQQxdnDq282IW0mysWDnGAQ0I8EMMJWQZMUVJ_74e6dqtE8O_YjjWgQzqOhP4V1isGBx8iJMiWzNMyxP84aObzeqLlyE78aJsMOl0z8fWj2pqya_FEuaToFHEcxZ3FJ9_U25-Aoag24zDNoTIllYrX6geCNO9PdaK1dLWKA2sMLZMZ58auzoI1qPy7uhviD25PX_PNrrI_XMZ0u2MBjc/http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists%2FGMX-Users_List
 before posting!

* Can't post? Read 
http://secure-web.cisco.com/1yt_VioDuTK5YDl9Q_jRUvWaeaLxVnxvdzuVuu9PFL0lNtvesrLx2OSpmohlMSWw_fb9QKrUp6QxYH-LoV5VtUO5caLkKdWpihSLYQbK5FmyRVVzsVYJhiT7OYx6wTjeYzKUw2Z0SpWtDnYsbGqql11QL7qT39jmxhd6xHd1bIhD7yIThKVXHcI4cJrOjqBTuMEDWLm7Xd5eLzGWHr_n58K9BQchkE3L4ymXEfoUa4c0/http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists

* For (un)subscribe requests visit
https://secure-web.cisco.com/1KMOCw8Kr5dUhkR-1S8WcbMa7DVZxUYsntzcAAfExbboYW-CEhCU2LLYhQsa4mzTaQ8FWv5KSJAAWxXI80xIwMUu8GDN-5InZw5iphCzhDvwjNOskv_FMTQuhJygoheWDld5UCSfx2SDnuSy-JhDkJZxqu-NfrSvk7SHwV9SCoicC62ET08z1LuzXERDyQ6D32dBCcWywTloaOKZwL_c5dR1JfmhryH_VVGr7GZi9O5E/https%3A%2F%2Fmaillist.sys.kth.se%2Fmailman%2Flistinfo%2Fgromacs.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 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.

[gmx-users] Barostat Selection

[Parker de Waal]

Hi everyone,

I recently got into an interesting discussion regarding barostat selection for 
NPT equilibration and later NPT production runs and was wondering what the 
community thought on this issue.

Specifically, for the initial NPT equilibrium, would it be acceptable to use 
the berendsen barostat (tau_p = 1.0 ) and then later switch to the 
Parrinello-Rahman barostat (tau_p = 5) for production, or would it be best to 
stick with berendsen (keep tau_p = 1.0 or increase to 5.0 to increase ns/day?)

Best,
Parker
-- 
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.

Re: [gmx-users] Barostat Selection

[Justin Lemkul]

On 9/29/15 8:57 PM, Parker de Waal wrote:

Hi everyone,

I recently got into an interesting discussion regarding barostat selection for 
NPT equilibration and later NPT production runs and was wondering what the 
community thought on this issue.

Specifically, for the initial NPT equilibrium, would it be acceptable to use 
the berendsen barostat (tau_p = 1.0 ) and then later switch to the 
Parrinello-Rahman barostat (tau_p = 5) for production, or would it be best to 
stick with berendsen (keep tau_p = 1.0 or increase to 5.0 to increase ns/day?)



Barostat relaxation time should have no effect on performance.  The Berendsen 
weak coupling algorithms do not produce correct distributions and they should 
not be used for production simulations.  The algorithm is good for 
equilibration, but shouldn't be used for much else.


-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.

Re: [gmx-users] Barostat Selection

[Justin Lemkul]

On 9/29/15 9:06 PM, Parker de Waal wrote:

Thank you for the prompt response Justin.

I was unaware that the relaxation time had no effect on simulation performance. 
Would you expect a difference between tau_p = 1.0 and 5.0 for production runs 
using Parrinello-Rahman?



Expect a difference with respect to what?  All you're doing is changing how 
quickly the barostat responds to changes in pressure.  Either value is probably 
fine for most purposes.


-Justin


-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin 
Lemkul
Sent: Tuesday, September 29, 2015 9:00 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Barostat Selection



On 9/29/15 8:57 PM, Parker de Waal wrote:

Hi everyone,

I recently got into an interesting discussion regarding barostat selection for 
NPT equilibration and later NPT production runs and was wondering what the 
community thought on this issue.

Specifically, for the initial NPT equilibrium, would it be acceptable
to use the berendsen barostat (tau_p = 1.0 ) and then later switch to
the Parrinello-Rahman barostat (tau_p = 5) for production, or would it
be best to stick with berendsen (keep tau_p = 1.0 or increase to 5.0
to increase ns/day?)



Barostat relaxation time should have no effect on performance.  The Berendsen 
weak coupling algorithms do not produce correct distributions and they should 
not be used for production simulations.  The algorithm is good for 
equilibration, but shouldn't be used for much else.

-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://secure-web.cisco.com/1ojLfbMlRYuefZ_1olbKjXPZp-h4B9atVOLOfNXQ7pczhcSv3VkmPlIgK3dmbOVGiGwMhCTCoZzv_jrbSSl3rJC35FBF34au6FR1lWqNwjUmLk1i-p8rHhXfjXJ8RiLsvoVuIxKtlum35oYjAa7eqmHBr2xfQ0a2cH-V3FI4YDUtttitIzcF1c177lFZnkxF9NEeJigdBkiDZVBjuINkIF7gVdNGETE1r8Eu6XjM24e4/http%3A%2F%2Fmackerell.umaryland.edu%2F%7Ejalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://secure-web.cisco.com/1MQxYm8ywdBbJUNmGzQcwWfpEQQxdnDq282IW0mysWDnGAQ0I8EMMJWQZMUVJ_74e6dqtE8O_YjjWgQzqOhP4V1isGBx8iJMiWzNMyxP84aObzeqLlyE78aJsMOl0z8fWj2pqya_FEuaToFHEcxZ3FJ9_U25-Aoag24zDNoTIllYrX6geCNO9PdaK1dLWKA2sMLZMZ58auzoI1qPy7uhviD25PX_PNrrI_XMZ0u2MBjc/http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists%2FGMX-Users_List
 before posting!

* Can't post? Read 
http://secure-web.cisco.com/1yt_VioDuTK5YDl9Q_jRUvWaeaLxVnxvdzuVuu9PFL0lNtvesrLx2OSpmohlMSWw_fb9QKrUp6QxYH-LoV5VtUO5caLkKdWpihSLYQbK5FmyRVVzsVYJhiT7OYx6wTjeYzKUw2Z0SpWtDnYsbGqql11QL7qT39jmxhd6xHd1bIhD7yIThKVXHcI4cJrOjqBTuMEDWLm7Xd5eLzGWHr_n58K9BQchkE3L4ymXEfoUa4c0/http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists

* For (un)subscribe requests visit
https://secure-web.cisco.com/1KMOCw8Kr5dUhkR-1S8WcbMa7DVZxUYsntzcAAfExbboYW-CEhCU2LLYhQsa4mzTaQ8FWv5KSJAAWxXI80xIwMUu8GDN-5InZw5iphCzhDvwjNOskv_FMTQuhJygoheWDld5UCSfx2SDnuSy-JhDkJZxqu-NfrSvk7SHwV9SCoicC62ET08z1LuzXERDyQ6D32dBCcWywTloaOKZwL_c5dR1JfmhryH_VVGr7GZi9O5E/https%3A%2F%2Fmaillist.sys.kth.se%2Fmailman%2Flistinfo%2Fgromacs.org_gmx-users
 or send a mail to gmx-users-requ...@gromacs.org.



--
==

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.

Re: [gmx-users] Analysis of old xtc file using gromacs-5 tools

[Teemu Murtola]

Hi,

I now changed the check to provide more details (in 5140
). If you haven't figured out what the
issue was, you could try building the source code from the above link, and
running it to get more details.

There is not much we can do to help diagnose the issue further, unless you
can provide additional information on the file system contents. Also note
that if you provide an input file name that looks like a valid file name
(with the correct extension), Gromacs 5.1 will use it as is, or give an
error if it does not exist. Previous versions silently tried to append all
kinds of extensions if the file did not exist (or could not be read) even
in such a case, and could then use some other file as input.

Best regards,
Teemu

On Sat, Sep 26, 2015 at 11:56 AM Teemu Murtola 
wrote:

> This error has nothing to do with the contents of the file, but rather the
> operating system appears to be telling Gromacs that the file cannot be
> opened or that it is not a regular file. With the information here, it's
> difficult to say anything more; if you want to debug this further, the
> relevant function is gmx::File::exists().
>
> It would be useful to know what's the problem so that the check (or the
> error message) can be improved.
>
> Best regards,
> Teemu
>
> On Fri, Sep 25, 2015, 21:20 Venkat Reddy  wrote:
>
>> Hi Tsjerk,
>> Thank you for the quick reply. Yes I can access it with other versions,
>> like 4.5.5, 5.0.4.
>>
>> On Fri, Sep 25, 2015 at 11:33 PM, Tsjerk Wassenaar 
>> wrote:
>>
>> > Hi Venkat,
>> >
>> > Does it exist? Is it accessible? The XTC format did not change since the
>> > early years of Gromacs. Can you access it with a different version?
>> >
>> > Cheers,
>> >
>> > Tsjerk
>> > On Sep 25, 2015 19:52, "Venkat Reddy"  wrote:
>> >
>> > > Dear all,
>> > > I have a trajectory file generated by gromacs-4.5.5. Recently I tried
>> to
>> > > plot radial distribution function using 'gmx rdf' tool available in
>> > > gromacs-5.1. But I am getting the following error.
>> > > Error in user input:
>> > > Invalid command-line options
>> > >   In command-line option -f
>> > > File 'system.xtc' does not exist or is not accessible.
>> > >
>> > > I knew that gromacs old trajectories can be analysed using new version
>> > > tools. But why I am facing this error?
>> > >
>> > >
>> > > With regards
>> > > Venkat Reddy Chirasani
>> > > PhD student
>> > > Laboratory of Computational Biophysics
>> > > Department of Biotechnology
>> > > IIT Madras
>> > > Chennai
>> > > INDIA-600036
>> > > --
>> > > 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 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.
>> >
>>
>>
>>
>> --
>> With Best Wishes
>> Venkat Reddy Chirasani
>> PhD student
>> Laboratory of Computational Biophysics
>> Department of Biotechnology
>> IIT Madras
>> Chennai
>> INDIA-600036
>> --
>> 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 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.

Re: [gmx-users] Analysis of old xtc file using gromacs-5 tools

[Venkat Reddy]

Hi Teemu,
Thank you for providing the patch. But the patched version is giving
following error message:

Program: gmx rdf, VERSION 5.2-dev
Source file: src/gromacs/utility/path.cpp (line 406)
Function:static void gmx::File::throwOnError(const
gmx::File::NotFoundInfo&)

System I/O error:
Failed to access file 'traj.xtc'.
The file could not be opened.
  Reason: Value too large for defined data type
  (call to fopen() returned error code 75)

I would like to inform you that I have installed this patched version to a
non-standard location.


On Wed, Sep 30, 2015 at 8:39 AM, Teemu Murtola 
wrote:

> Hi,
>
> I now changed the check to provide more details (in 5140
> ). If you haven't figured out what the
> issue was, you could try building the source code from the above link, and
> running it to get more details.
>
> There is not much we can do to help diagnose the issue further, unless you
> can provide additional information on the file system contents. Also note
> that if you provide an input file name that looks like a valid file name
> (with the correct extension), Gromacs 5.1 will use it as is, or give an
> error if it does not exist. Previous versions silently tried to append all
> kinds of extensions if the file did not exist (or could not be read) even
> in such a case, and could then use some other file as input.
>
> Best regards,
> Teemu
>
> On Sat, Sep 26, 2015 at 11:56 AM Teemu Murtola 
> wrote:
>
> > This error has nothing to do with the contents of the file, but rather
> the
> > operating system appears to be telling Gromacs that the file cannot be
> > opened or that it is not a regular file. With the information here, it's
> > difficult to say anything more; if you want to debug this further, the
> > relevant function is gmx::File::exists().
> >
> > It would be useful to know what's the problem so that the check (or the
> > error message) can be improved.
> >
> > Best regards,
> > Teemu
> >
> > On Fri, Sep 25, 2015, 21:20 Venkat Reddy  wrote:
> >
> >> Hi Tsjerk,
> >> Thank you for the quick reply. Yes I can access it with other versions,
> >> like 4.5.5, 5.0.4.
> >>
> >> On Fri, Sep 25, 2015 at 11:33 PM, Tsjerk Wassenaar 
> >> wrote:
> >>
> >> > Hi Venkat,
> >> >
> >> > Does it exist? Is it accessible? The XTC format did not change since
> the
> >> > early years of Gromacs. Can you access it with a different version?
> >> >
> >> > Cheers,
> >> >
> >> > Tsjerk
> >> > On Sep 25, 2015 19:52, "Venkat Reddy"  wrote:
> >> >
> >> > > Dear all,
> >> > > I have a trajectory file generated by gromacs-4.5.5. Recently I
> tried
> >> to
> >> > > plot radial distribution function using 'gmx rdf' tool available in
> >> > > gromacs-5.1. But I am getting the following error.
> >> > > Error in user input:
> >> > > Invalid command-line options
> >> > >   In command-line option -f
> >> > > File 'system.xtc' does not exist or is not accessible.
> >> > >
> >> > > I knew that gromacs old trajectories can be analysed using new
> version
> >> > > tools. But why I am facing this error?
> >> > >
> >> > >
> >> > > With regards
> >> > > Venkat Reddy Chirasani
> >> > > PhD student
> >> > > Laboratory of Computational Biophysics
> >> > > Department of Biotechnology
> >> > > IIT Madras
> >> > > Chennai
> >> > > INDIA-600036
> >> > > --
> >> > > 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 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.
> >> >
> >>
> >>
> >>
> >> --
> >> With Best Wishes
> >> Venkat Reddy Chirasani
> >> PhD student
> >> Laboratory of Computational Biophysics
> >> Department of Biotechnology
> >> IIT Madras
> >> Chennai
> >> INDIA-600036
> >> --
> >> 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 

Re: [gmx-users] Pausing and resuming mdrun

[Szilárd Páll]

The combination of STOP and CONT signals should work just fine - the only
negative effect will be incorrect cycle counting output in the log file.
You can also adjust the checkpointing frequency with -cpt if you e.g. want
a shorter interval.

In general, you can refer to types of signals with their name with/without
the SIG prefix or using the corresponding numeric value (e.g. KILL,
SIGKILL, or 9). For more I suggest checking:
- man kill
- https://en.wikipedia.org/wiki/Unix_signal#POSIX_signals

Cheers,
--
Szilárd

On Tue, Sep 29, 2015 at 7:28 PM, Andrew DeYoung 
wrote:

> Hi,
>
> I'm running an MD simulation using mdrun (specifically version 4.5.5 -- an
> old version).  I would like to pause this simulation -- perhaps for days
> or weeks -- so that I can run a different one on this node.
>
> Of course, one way is to just kill the simulation altogether:
>
> kill $ProcessID
>
> where $ProcessID is the process ID of the simulation.  Then, when I want
> to resume the simulation, I can just pass the last checkpoint file to
> mdrun.  Checkpoint files have been written every 15 minutes (i.e., the
> default setting), so with this method I will lose at most 15 minutes of
> computation time.
>
> But, is there any way to literally _pause_ the simulation and resume it a
> few days or weeks later?
>
> A Unix/Linux question and answer site (
>
> http://unix.stackexchange.com/questions/2107/how-to-suspend-and-resume-processes
> ) says that one can pause/resume a process with this method:
>
> kill -SIGSTOP $ProcessID
> kill -SIGCONT $ProcessID
>
> or:
>
> kill -SIGSTP $ProcessID
> kill -SIGCONT $ProcessID
>
> Another site ( http://www.cyberciti.biz/faq/unix-kill-command-examples/ )
> says to just use:
>
> kill -STOP $ProcessID
> kill -CONT $ProcessID
>
> My question is, do you think that these Linux methods will work with
> mdrun?  I did a test with mdrun on another node, and it seems to work, but
> I'm just wondering if there are any dangers in using these methods.
>
> (I am accessing the Linux machine remotely, by SSH.  Sometimes my SSH
> connection gives out, so when starting a simulation I always use "nohup
> mdrun -s topol.tpr" so that the mdrun process is not terminated when my
> SSH connection flakes out.  I'm not sure if this will affect the viability
> of the "kill -STOP/CONT" method...)
>
> Thanks so much,
>
> Andrew DeYoung
> Carnegie Mellon University
>
> --
> 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 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.