On 11/11/13 11:24 AM, Carlos Javier Almeciga Diaz wrote:
Hello evryone,
I doing a simulation of a ligand-protein interaction with gromacs 4.5.5.
Everything looks fine after I equilibrate the protein-ligand complex. I'm
running these commands:
grompp -f nvt.mdp -c em.gro -p topol.top -n
Hello evryone,
I doing a simulation of a ligand-protein interaction with gromacs 4.5.5.
Everything looks fine after I equilibrate the protein-ligand complex. I'm
running these commands:
grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr
mdrun -deffnm nvt
Nevertheless, I got
Hi,
My heteromolecule structure is missing hydrogens. I did an aminoacids.hdb
entry which I suppose being right. When running `g_protonate -s conf.pdb -o
prot.pdb` to add the hydrogens happens an segmentation fault. The traceback
for 4.6.4-dev-20130808-afc6131 follows. I could add them by any
On 8/9/13 2:35 PM, Pedro Lacerda wrote:
Hi,
My heteromolecule structure is missing hydrogens. I did an aminoacids.hdb
entry which I suppose being right. When running `g_protonate -s conf.pdb -o
prot.pdb` to add the hydrogens happens an segmentation fault. The traceback
for
Dear all
I want to study the diffusion coeffcient of CO in water. I have done the
energy minimization step and got the problem segmentation fault during
Equilibration. I am confused whether my input file has
got some error or the error is in the processing machine.I have made
On 6/6/13 4:45 AM, Ishwor Poudyal wrote:
Dear all
I want to study the diffusion coeffcient of CO in water. I have done the
energy minimization step and got the problem segmentation fault during
Equilibration. I am confused whether my input file has
got some error or the
Sir,
I am doing membrane protein dynamics in lipid bilayer, using oplsaa
force field. When I am doing minimization after genion I getting message
like this
Back Off! I just backed up ions_1.tpr.trr to ./#ions_1.tpr.trr.2#
ack Off! I just backed up ions_1.tpr.edr to
Sir,
I have one more doubt. During NVT equilibration mdrun giving
segmentation fault and not generating any gro files and generating two pdb
files. The message is like this
Wrote pdb files with previous and current coordinates
Warning: 1-4 interaction between 485 and 490 at distance
On 11/29/12 10:44 AM, Shine A wrote:
Sir,
I have one more doubt. During NVT equilibration mdrun giving
segmentation fault and not generating any gro files and generating two pdb
files. The message is like this
Wrote pdb files with previous and current coordinates
Warning: 1-4
Hello all,
I was trying to calculate solvent mediated H-bond between a amino acid
residue (Tyr) and solvent molecule present within cutoff of 0.5nm (after
creating separate index) with the help of g_hbond version 4.5.3. But I am
getting segmentation fault while running g_hbond. Moreover I am
There were a few bugfixes done to g_hbond since 4.5.3. Try a more recent
version.
Erik
23 okt 2012 kl. 17.41 skrev bipin singh:
Hello all,
I was trying to calculate solvent mediated H-bond between a amino acid
residue (Tyr) and solvent molecule present within cutoff of 0.5nm (after
So I have spent the past few weeks debugging my equilibration protocols,
which were an odd hybrid of examples ranging from GROMACS 3.3 up to GROMACS
4.5. I have cleaned out old code. I added an in vacuo energy minimization
step for the protein without solvent, and a missing NVT step after
Thanks very much for much for your help. The Carbon naotube issue is solved. I
still have to figure out the polymers. Thanks for the info
Regards
Elie
Date: Fri, 14 Sep 2012 10:31:28 -0400
From: jalem...@vt.edu
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Segmentation fault (core
On 9/14/12 12:19 AM, Elie M wrote:
Dear all, I am trying to study the MD of a Carbon Nanotube interacting with
some polymers. and I have some problems in forming the topology files. I have
actually two questions and I hope you can help me in that.
(1) In an attempt to form the topology
Dear all, I am trying to study the MD of a Carbon Nanotube interacting with
some polymers. and I have some problems in forming the topology files. I have
actually two questions and I hope you can help me in that.
(1) In an attempt to form the topology files of CNTs and graphene (using
x2top),
Dear All
I am trying to perform the azide ion in water simulation with
Gromacs. I generated to topology file with PRODG server for azide ion
and ran the calculations.I got one error at grompp level which was
327 non-matching atom names
atom names from azide.top will be used
atom names
On 8/21/12 6:00 AM, Deepak Ojha wrote:
Dear All
I am trying to perform the azide ion in water simulation with
Gromacs. I generated to topology file with PRODG server for azide ion
and ran the calculations.I got one error at grompp level which was
327 non-matching atom names
atom
at yahoo.com
To: Discussion list for GROMACS users gmx-users at gromacs.org
Sent: Tuesday, 19 June 2012, 12:04
Subject: [gmx-users] segmentation fault-g_spatial
Dear Gromacs users.
I have a protein in a box of water. I want to calculate the SDF of water
molecules around the protein. I have used
- Forwarded Message -
From: delara aghaie d_agh...@yahoo.com
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Tuesday, 19 June 2012, 12:04
Subject: [gmx-users] segmentation fault-g_spatial
Dear Gromacs users.
I have a protein in a box of water. I want to calculate
On 6/19/12 9:34 AM, delara aghaie wrote:
- Forwarded Message -
*From:* delara aghaie d_agh...@yahoo.com
*To:* Discussion list for GROMACS users gmx-users@gromacs.org
*Sent:* Tuesday, 19 June 2012, 12:04
*Subject:* [gmx-users] segmentation fault-g_spatial
Dear Gromacs users.
I have
Dear Gmx Users,
I created a plane surface made of 4 different atoms (400 atoms togehter).
Each atom correspond to different residue - I added them to the
aminoacids.rtp file. They are placed in different positions with LJ radius
of 1.7A and they their center is 3.6 A away from each other (0.2A
Dear gmx users,
I am simulating a system including carbon nanotube(a finite
one)+water+surfactant and so far I have done these things:
1.I generated the topology of CNT ( opls force field) by this command:
g_x2top -f cnt.pdf -o cnt.top -nopairs -nexcl 3 -name CNT
2.I used TopolGen to produce
On 5/1/12 7:19 AM, niaz poorgholami wrote:
Dear gmx users,
I am simulating a system including carbon nanotube(a finite
one)+water+surfactant and so far I have done these things:
1.I generated the topology of CNT ( opls force field) by this command:
g_x2top -f cnt.pdf -o cnt.top -nopairs -nexcl
thank you Sir for your reply.below I provide you .mdp file:
title = UNK-ligand complex NVT equilibration
define = -DPOSRES -DPOSRES_LIG ; position restrain the UNK and LIG
; Run parameters
integrator = md; leap-frog integrator
nsteps = 5; 2 * 5 = 100 ps
dt
On 5/1/12 1:13 PM, niaz poorgholami wrote:
thank you Sir for your reply.below I provide you .mdp file:
title = UNK-ligand complex NVT equilibration
define = -DPOSRES -DPOSRES_LIG ; position restrain the UNK and LIG
; Run parameters
integrator = md; leap-frog integrator
Dear Justin
the results of EM was:
Steepest Descents converged to Fmax 1000 in 77 steps
Potential Energy = -3.6802272e+05
Maximum force = 8.9652832e+02 on atom 1556
Norm of force = 1.1512711e+02
thank you for your concern
--
gmx-users mailing listgmx-users@gromacs.org
On 5/1/12 2:50 PM, niaz poorgholami wrote:
Dear Justin
the results of EM was:
Steepest Descents converged to Fmax 1000 in 77 steps
Potential Energy = -3.6802272e+05
Maximum force = 8.9652832e+02 on atom 1556
Norm of force = 1.1512711e+02
thank you for your concern
All of that
priya thiyagarajan wrote:
hello sir,
thanks for your kind reply..
in another folder i resubmitted my mdrun from starting time..
i reduced my time step..
i kept my time step = 0.001
this is my md.mdp file
title= Gromacs43a1 lipopeptide MD
; Run parameters
integrator= md
mailto:gmx-users@gromacs.org
Date: Wed, 28 Mar 2012 13:29:40 +1100
To: Discussion list for GROMACS users gmx-users@gromacs.org
mailto:gmx-users@gromacs.org
Subject: Re: [gmx-users] Segmentation Fault using g_cluster
On 28/03/2012 1:00 PM, Davide Mercadante wrote:
Dear Gromacs Users,
I am trying
Dear Gromacs Users,
I am trying to run g_cluster to find an average structure for my system and
after giving the following command line:
g_cluster_d -f allnj10_XM10.xtc -s EB_XM.gro -cl pdb_ligplot_XM.pdb -n g
g_cluster started without problems and continued calculating the matrix
etcuntil I
On 28/03/2012 1:00 PM, Davide Mercadante wrote:
Dear Gromacs Users,
I am trying to run g_cluster to find an average structure for my
system and after giving the following command line:
g_cluster_d -f allnj10_XM10.xtc -s EB_XM.gro -cl pdb_ligplot_XM.pdb -n --g
g_cluster started without
for GROMACS users gmx-users@gromacs.org
Date: Wed, 28 Mar 2012 13:29:40 +1100
To: Discussion list for GROMACS users gmx-users@gromacs.org
Subject: Re: [gmx-users] Segmentation Fault using g_cluster
On 28/03/2012 1:00 PM, Davide Mercadante wrote:
Dear Gromacs Users,
I am trying
Hi all
Would you please let me know how can I remove the following error when I
want to run 'mdrun -v -deffnm H'?
Back Off! I just backed up H.log to ./#H.log.1#
Getting Loaded...
Reading file H.tpr, VERSION 4.5.4 (single precision)
Starting 24 threads
Segmentation fault
Thanks
Regards
Saly
saly jackson wrote:
Hi all
Would you please let me know how can I remove the following error when I
want to run 'mdrun -v -deffnm H'?
Back Off! I just backed up H.log to ./#H.log.1#
Getting Loaded...
Reading file H.tpr, VERSION 4.5.4 (single precision)
Starting 24 threads
Segmentation
Hi ,
Thank you for help.
I solve my problem for LINCS error
But now I have another problem
after mdrun command
gromacs output
Making 1D domain decomposition 4 x 1 x 1
starting mdrun 'Martini system from nap.pdb'
5000 steps,100.0 ps.
step 0Segmentation fault
Please give the valuable
On 9/03/2012 6:24 PM, rama david wrote:
Hi ,
Thank you for help.
I solve my problem for LINCS error
But now I have another problem
after mdrun command
gromacs output
Making 1D domain decomposition 4 x 1 x 1
starting mdrun 'Martini system from nap.pdb'
5000 steps,100.0 ps.
step
Dear gmx-users,
I'm facing segmentation fault error while *mdrun*.
When i checked my md.log file, after 440'th step the kinetic energy energy
increases by tenfold and hence the temperature (temp - 6.80141e+01K to
2.21829e+02K). all other values, potential energy etc. are not changing much so
i
On 6/03/2012 2:58 AM, shilpa yadahalli wrote:
Dear gmx-users,
I'm facing segmentation fault error while *mdrun*.
When i checked my md.log file, after 440'th step the kinetic energy
energy increases by tenfold and hence the temperature (temp -
6.80141e+01K to 2.21829e+02K). all other values,
Dear Gmx Users,
I am trying to run nvt simulation (equilibration) of the protein in
implicit solvent. My mdp:
integrator = md ; leap-frog integrator
nsteps = 100 ; 0.0005 * 100 = 0.5 ns
dt = 0.0005 ; 0.5 fs
; Output control
nstxout = 1
nstxtcout = 1 ; xtc compressed
Steven Neumann wrote:
Dear Gmx Users,
I am trying to run nvt simulation (equilibration) of the protein in
implicit solvent. My mdp:
integrator = md ; leap-frog integrator
nsteps = 100 ; 0.0005 * 100 = 0.5 ns
dt = 0.0005 ; 0.5 fs
; Output control
nstxout = 1
nstxtcout =
On Thu, Mar 1, 2012 at 2:55 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Steven Neumann wrote:
Dear Gmx Users,
I am trying to run nvt simulation (equilibration) of the protein in
implicit solvent. My mdp:
integrator = md ; leap-frog integrator
nsteps = 100 ; 0.0005 * 100 = 0.5
On Thu, Mar 1, 2012 at 3:32 PM, Steven Neumann s.neuman...@gmail.comwrote:
On Thu, Mar 1, 2012 at 2:55 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Steven Neumann wrote:
Dear Gmx Users,
I am trying to run nvt simulation (equilibration) of the protein in
implicit solvent. My mdp:
On Thu, Mar 1, 2012 at 3:58 PM, Steven Neumann s.neuman...@gmail.comwrote:
On Thu, Mar 1, 2012 at 3:32 PM, Steven Neumann s.neuman...@gmail.comwrote:
On Thu, Mar 1, 2012 at 2:55 PM, Justin A. Lemkul jalem...@vt.eduwrote:
Steven Neumann wrote:
Dear Gmx Users,
I am trying to run
Steven Neumann wrote:
On Thu, Mar 1, 2012 at 3:58 PM, Steven Neumann s.neuman...@gmail.com
mailto:s.neuman...@gmail.com wrote:
On Thu, Mar 1, 2012 at 3:32 PM, Steven Neumann
s.neuman...@gmail.com mailto:s.neuman...@gmail.com wrote:
On Thu, Mar 1, 2012 at 2:55 PM,
On Thu, Mar 1, 2012 at 5:43 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Steven Neumann wrote:
On Thu, Mar 1, 2012 at 3:58 PM, Steven Neumann s.neuman...@gmail.commailto:
s.neuman...@gmail.com** wrote:
On Thu, Mar 1, 2012 at 3:32 PM, Steven Neumann
s.neuman...@gmail.com
Steven Neumann wrote:
On Thu, Mar 1, 2012 at 5:43 PM, Justin A. Lemkul jalem...@vt.edu
mailto:jalem...@vt.edu wrote:
Steven Neumann wrote:
On Thu, Mar 1, 2012 at 3:58 PM, Steven Neumann
s.neuman...@gmail.com mailto:s.neuman...@gmail.com
On Thu, Mar 1, 2012 at 10:07 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Steven Neumann wrote:
On Thu, Mar 1, 2012 at 5:43 PM, Justin A. Lemkul jalem...@vt.edumailto:
jalem...@vt.edu wrote:
Steven Neumann wrote:
On Thu, Mar 1, 2012 at 3:58 PM, Steven Neumann
On 2/03/2012 9:22 AM, Steven Neumann wrote:
On Thu, Mar 1, 2012 at 10:07 PM, Justin A. Lemkul jalem...@vt.edu
mailto:jalem...@vt.edu wrote:
Steven Neumann wrote:
On Thu, Mar 1, 2012 at 5:43 PM, Justin A. Lemkul
jalem...@vt.edu mailto:jalem...@vt.edu
On Thu, Mar 1, 2012 at 10:26 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 2/03/2012 9:22 AM, Steven Neumann wrote:
On Thu, Mar 1, 2012 at 10:07 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Steven Neumann wrote:
On Thu, Mar 1, 2012 at 5:43 PM, Justin A. Lemkul
Dear Gromacs Experts,
I am having problem in execution of a command in Gromacs,
thats when i use dssp for secondary structure analysis.
it gives error:
Reading file md_0_10.tpr, VERSION 4.5.5 (single precision)
Reading file md_0_10.tpr, VERSION 4.5.5 (single precision)
Segmentation fault (core
On 2/01/2012 12:35 AM, Saba Ferdous wrote:
Dear Gromacs Experts,
I am having problem in execution of a command in Gromacs,
thats when i use dssp for secondary structure analysis.
it gives error:
Reading file md_0_10.tpr, VERSION 4.5.5 (single precision)
Reading file md_0_10.tpr, VERSION
Hi,
I encounter the following error when trying to execute mdrun:
# Running Gromacs: read TPR and write output to /gpfs disk
$MPIRUN $MDRUN -v -nice 0 -np $NSLOTS \
-s n12_random_50_protein_all.tpr \
-o n12_random_50_protein_all.trr \
-c n12_random_50_protein_all.gro \
-g
On 8/12/2011 7:36 AM, rainy908 wrote:
Hi,
I encounter the following error when trying to execute mdrun:
# Running Gromacs: read TPR and write output to /gpfs disk
$MPIRUN $MDRUN -v -nice 0 -np $NSLOTS \
-s n12_random_50_protein_all.tpr \
-o n12_random_50_protein_all.trr \
-c
Thank you, Mark.
Using GMX_NOOPTIMIZEDKERNELS=1 everything runs fine on power6.
I also tried to run on a linux cluster and it went ok.
Fabio
The most likely issue is some normal blowing up scenario leading to a
table-lookup-overrun segfault in the 3xx series kernels. I don't know
why the
On 3/11/2011 7:59 PM, Fabio Affinito wrote:
Thank you, Mark.
Using GMX_NOOPTIMIZEDKERNELS=1 everything runs fine on power6.
I also tried to run on a linux cluster and it went ok.
Sounds like a bug. Please file a report here http://redmine.gromacs.org
http://redmine.gromacs.org/ including your
: Giovedì, 3 novembre 2011 14:40:39
Oggetto: Re: [gmx-users] segmentation fault from power6 kernel
On 3/11/2011 7:59 PM, Fabio Affinito wrote:
Thank you, Mark.
Using GMX_NOOPTIMIZEDKERNELS=1 everything runs fine on power6.
I also tried to run on a linux cluster and it went ok.
Sounds like a bug
Dear all,
I've trying to run a simulation on a IBM Power6 cluster. At the
beginning of the simulation I've got a segmentation fault. I investigated with
TotalView and I've found that this segmentation violation originates in the
pwr6kernel310.F
Up to now, I still didn't find what is behind this
Hi
When i perform mdrun for energy minimization, I found an error revealed
segmentation fault. Please explain me
--
**
Ithayaraja M,
Research Scholar,
Department of Bionformatics,
Bharathiar University,
Coimbatore 641 046,
Tamil Nadu
India
--
gmx-users mailing listgmx-users@gromacs.org
Dear gmx-users:
Thanks Justin for your help. But now I am experiencing a Segmentation fault
error when executing mdrun. I've perused the archives but found none of the
threads on segmentation faults similar to my case here. I believe the
segmentation fault is caused by the awkward
rainy908 wrote:
Dear gmx-users:
Thanks Justin for your help. But now I am experiencing a Segmentation fault
error when executing mdrun. I've perused the archives but found none of the
threads on segmentation faults similar to my case here. I believe the
segmentation fault is caused by
Hi Justin,
THanks for the input. So I traced back to my energy minimization steps, and am
getting the error message after I execute the following line:
$mdrun -s 1JFF_em.tpr -o 1JFF_em.trr -c 1JFF_b4pr.gro -e em.edr
output:
Back Off! I just backed up md.log to ./#md.log.2#
Reading file
On 18/08/2011 2:41 PM, rainy908 wrote:
Hi Justin,
THanks for the input. So I traced back to my energy minimization steps, and am
getting the error message after I execute the following line:
$mdrun -s 1JFF_em.tpr -o 1JFF_em.trr -c 1JFF_b4pr.gro -e em.edr
output:
Back Off! I just backed up
Hello All,
I was trying to run a MD simulation of a 17 amino acid peptide. At the
position restraint step, the program crashed after running ~536 ps.
It gave the error message:
t=536.242 ps: Water molecule starting at atom 6101 cannot be settled.
Check for bad contacts and/or reduce the
Sayan Bagchi wrote:
Hello All,
I was trying to run a MD simulation of a 17 amino acid peptide. At the
position restraint step, the program crashed after running ~536 ps.
It gave the error message:
t=536.242 ps: Water molecule starting at atom 6101 cannot be settled.
Check for bad contacts
dear gmx-users,
During equilibriation i get the following error.Any
suggestions please.
*grompp*
WARNING 1 [file npt.mdp]:
The sum of the two largest charge group radii (2.369582) is larger than
rlist (1.00)
This run will generate roughly 73 Mb of data
There
sreelakshmi ramesh wrote:
dear gmx-users,
During equilibriation i get the following
error.Any suggestions please.
*grompp*
WARNING 1 [file npt.mdp]:
The sum of the two largest charge group radii (2.369582) is larger than
rlist (1.00)
This message
Dear All,
I am using the gromacs 4.0.7 version and I was trying to calculate the
momentum autocorrelation function by using the -m flag. However, I get a
segmentation fault as follows:
trn version: GMX_trn_file (double precision)
Reading frame 0 time0.000 Segmentation fault
When I
Vigneshwar Ramakrishnan wrote:
Dear All,
I am using the gromacs 4.0.7 version and I was trying to calculate the
momentum autocorrelation function by using the -m flag. However, I get a
segmentation fault as follows:
trn version: GMX_trn_file (double precision)
Reading frame 0 time
Hi,
apparently this bug fix made it to 4.5, but not to 4.0.
I will apply the fix also there.
Carsten
On Feb 1, 2011, at 1:58 PM, Justin A. Lemkul wrote:
Vigneshwar Ramakrishnan wrote:
Dear All,
I am using the gromacs 4.0.7 version and I was trying to calculate the
momentum
Hi Vigneshwar,
the problem is fixed now in the release-4-0-patches branch.
Carsten
On Feb 1, 2011, at 2:00 PM, Carsten Kutzner wrote:
Hi,
apparently this bug fix made it to 4.5, but not to 4.0.
I will apply the fix also there.
Carsten
On Feb 1, 2011, at 1:58 PM, Justin A. Lemkul
Thanks very much, Dr. Kutzner!
On Tue, Feb 1, 2011 at 9:14 PM, Carsten Kutzner ckut...@gwdg.de wrote:
Hi Vigneshwar,
the problem is fixed now in the release-4-0-patches branch.
Carsten
On Feb 1, 2011, at 2:00 PM, Carsten Kutzner wrote:
Hi,
apparently this bug fix made it to 4.5,
Dear all,
I launched on my system a first simulation of 5 ns, then I prolonged it to
50 ns using
tpbconv -s tpr1_5ns.tpr -until 5 -o tpr2_50ns.tpr
and then
mdrun -s tpr2_50ns.tpr -deffnm md2_50ns -cpi md1_5ns.cpt
Since my simulation was interrupted several times, every time I relaunched
it
Anna Marabotti wrote:
Dear all,
I launched on my system a first simulation of 5 ns, then I prolonged it
to 50 ns using
tpbconv -s tpr1_5ns.tpr -until 5 -o tpr2_50ns.tpr
and then
mdrun -s tpr2_50ns.tpr -deffnm md2_50ns -cpi md1_5ns.cpt
Since my simulation was interrupted several times,
Hi all,
I have been running alot of simulations on protein ligand interactions, and my settings/setup/mdp files worked great for one system. Then when we moved to a larger and more complicated system we started getting mdrun segmentation faults during steep energy
TJ Mustard wrote:
Hi all,
I have been running alot of simulations on protein ligand interactions,
and my settings/setup/mdp files worked great for one system. Then when
we moved to a larger and more complicated system we started getting
mdrun segmentation faults during steep energy
On January 17, 2011 at 1:20 PM Justin A. Lemkul jalem...@vt.edu wrote:
TJ Mustard wrote:
Hi all,
I have been running alot of simulations on protein ligand interactions,
and my
TJ Mustard wrote:
On January 17, 2011 at 1:20 PM Justin A. Lemkul jalem...@vt.edu wrote:
TJ Mustard wrote:
Hi all,
I have been running alot of simulations on protein ligand interactions,
and my settings/setup/mdp files worked great for one system. Then
I have Gromacs 4.0.7 I have simulated 1000 atoms of Argon with Lenard Jones
potential in a cubic box with linear size of 3.34. but when I reduced units
I confront with this error
Back Off! I just backed up md.log to ./#md.log.5#
Reading file argon.tpr, VERSION 4.0.7 (single precision)
Back Off! I
On 15/01/2011 8:50 PM, leila separdar wrote:
I have Gromacs 4.0.7 I have simulated 1000 atoms of Argon with Lenard
Jones potential in a cubic box with linear size of 3.34. but when I
reduced units I confront with this error
Back Off! I just backed up md.log to ./#md.log.5#
Reading file
I managed to run my simulation but which kind of coulomtype can I use except
PME? also I get different averages for kinetic and potential energies than
before reducing units I think these numbers must be the same because
E*=E/epsilon (epsilon is about 0.9977) for argon. could u please help me
Dear gromacs users
I used g_hbond tool for hydrogen bond analysis between protein and solvent
(water molecules).
I have encountered with :
Select a group: 3
Selected 3: 'Protein'
Select a group: 15
Selected 15: 'SOL'
Checking for overlap in atoms between Protein and SOL
Calculating hydrogen
Hi,
Upgrade to 4.5.x and see if the problem persists. I've hacked g_hbond
quite a bit since 4.0.5.
Erik
leila karami skrev 2010-12-18 14.02:
Dear gromacs users
I'm using gromacs 4.0.5. with following command:
g_hbond -f .xtc -s .tpr -n .ndx -num -g -hbn.
my system contains protein, dna
Dear Erik
I used g_hbond in 4.5.1 but problem was not solved.
--
Leila Karami
Ph.D. student of Physical Chemistry
K.N. Toosi University of Technology
Theoretical Physical Chemistry Group
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Dear Erik
thanks for your attention.
in version 4.5.1, when I use g_hbond -f .xtc -s .tpr -n .ndx -num -g -hbn,
gromacs give me only hbnum.xvg with segmentation fault.
when I use g_hbond -f .xtc -s .tpr -n .ndx -num -g, gromacs give me only
hbnum.xvg without segmentation fault.
how to file a
leila karami skrev 2010-12-18 15.38:
Dear Erik
thanks for your attention.
in version 4.5.1, when I use g_hbond -f .xtc -s .tpr -n .ndx -num -g
-hbn, gromacs give me only hbnum.xvg with segmentation fault.
when I use g_hbond -f .xtc -s .tpr -n .ndx -num -g, gromacs give me
only hbnum.xvg
Erik Marklund skrev 2010-12-18 15.40:
leila karami skrev 2010-12-18 15.38:
Dear Erik
thanks for your attention.
in version 4.5.1, when I use g_hbond -f .xtc -s .tpr -n .ndx -num -g
-hbn, gromacs give me only hbnum.xvg with segmentation fault.
when I use g_hbond -f .xtc -s .tpr -n .ndx -num
Dear Erik
excuse me, I sent .xtc and .tpr file your e-mail.
--
Leila Karami
Ph.D. student of Physical Chemistry
K.N. Toosi University of Technology
Theoretical Physical Chemistry Group
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
leila karami skrev 2010-12-18 16.18:
Dear Erik
excuse me, I sent .xtc and .tpr file your e-mail.
--
Leila Karami
Ph.D. student of Physical Chemistry
K.N. Toosi University of Technology
Theoretical Physical Chemistry Group
I can reproduce the segfault. It doesn't happen without -hbn. I'll
Erik Marklund skrev 2010-12-18 16.23:
leila karami skrev 2010-12-18 16.18:
Dear Erik
excuse me, I sent .xtc and .tpr file your e-mail.
--
Leila Karami
Ph.D. student of Physical Chemistry
K.N. Toosi University of Technology
Theoretical Physical Chemistry Group
I can reproduce the segfault.
Erik Marklund skrev 2010-12-18 16.36:
Erik Marklund skrev 2010-12-18 16.23:
leila karami skrev 2010-12-18 16.18:
Dear Erik
excuse me, I sent .xtc and .tpr file your e-mail.
--
Leila Karami
Ph.D. student of Physical Chemistry
K.N. Toosi University of Technology
Theoretical Physical
Dear Erik
there are several hb-per-pHist in gmx_hbond.c.
please say me exactly in which part of the gmx_hbond.c file if-statement
should be placed?
If I install gromacs 4.5.2 or 4.5.3, is there not this problem (segmentation
fault)?
--
Leila Karami
Ph.D. student of Physical Chemistry
K.N.
leila karami skrev 2010-12-18 16.52:
Dear Erik
there are several hb-per-pHist in gmx_hbond.c.
please say me exactly in which part of the gmx_hbond.c file
if-statement should be placed?
If I install gromacs 4.5.2 or 4.5.3, is there not this problem
(segmentation fault)?
--
Leila Karami
Erik Marklund skrev 2010-12-18 21.15:
leila karami skrev 2010-12-18 16.52:
Dear Erik
there are several hb-per-pHist in gmx_hbond.c.
please say me exactly in which part of the gmx_hbond.c file
if-statement should be placed?
If I install gromacs 4.5.2 or 4.5.3, is there not this problem
Erik Marklund wrote:
leila karami skrev 2010-12-18 16.52:
Dear Erik
there are several hb-per-pHist in gmx_hbond.c.
please say me exactly in which part of the gmx_hbond.c file
if-statement should be placed?
If I install gromacs 4.5.2 or 4.5.3, is there not this problem
(segmentation
Dear friends:Running several simulations, we have found a problem with the 'g_traj' utility. It doesn't finish properly the files it generates, and gives a segmentation fault. This is what we have done:We are working with double precision. With the file .mdp that is at the end of the mail, we have
Jorge Alberto Jover Galtier wrote:
Dear friends:
Running several simulations, we have found a problem with the 'g_traj'
utility. It doesn't finish properly the files it generates, and gives a
segmentation fault. This is what we have done:
We are working with double precision. With the file
Hello,
I am trying to calculate the dielectric constant for pure tetrahydrofuran
(THF) at 298K. I keep running into problems though. I have looked through
the gmx user list to see if others have had these problems, but I didn't see
any mention of them (although I did see that others were asked
Dear Justin,
1- Could you please check if I have grouped atoms properly? Lastly, I could
generate the tpr file for PR step. Since I am getting segmentation fault in
the next step I though maybe there is sth wring with charge groups..
However, I have a funda,mental question. I am to compute
Moeed wrote:
Dear Justin,
1- Could you please check if I have grouped atoms properly? Lastly, I
could generate the tpr file for PR step. Since I am getting segmentation
fault in the next step I though maybe there is sth wring with charge
groups..
I don't know how your labeling is set up.
Hi
I am facing this strange problem of segmentation fault while executing
mpi-enabled gromacs executables on remote server.
I source GMXRC, so that I can access executables from any directory without
specifying full path of gromacs/bin. And when I execute, say grompp, I get
segmentation fault.
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