[gmx-users] Ligand Topologies
Dear Users, I am trying to do Protein-Ligand MD simulations using GROMACS. I have tried to build topology files of my ligands using external tools like PRODRG server. I tried to correct the charges in line with Dr. Justin's paper *Practical Considerations for Building GROMOS-Compatible Small-Molecule Topologies, *but seems i cannot find the way, as the system crashes down during the solvating stage with an error message;* the net charge of my structure is not an integer value. * I will be glad to get any assistance. Thank you. -- *MUSYOKA THOMMAS MUTEMI Mob nos **+27844846540** B.Sc Biochemistry (Kenyatta University),MSc Pharmaceutical Science (Nagasaki University)* *PhD Student-Bioinformatics (Rhodes University) *Skype ID- MUSYOKA THOMMAS MUTEMI Alternative email - thom...@sia.co.ke * Do all the good you can, By all the means you can, In all the ways you can, In all the places you can, At all the times you can, To all the people you can, As long as ever you can. - John Wesley. * -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Ligand Topologies
Find out why your charge is not integral! Read all the output of whatever tool built the .itp file and reconsider your choices. Mark On Mon, Sep 9, 2013 at 9:46 AM, MUSYOKA THOMMAS mutemibiochemis...@gmail.com wrote: Dear Users, I am trying to do Protein-Ligand MD simulations using GROMACS. I have tried to build topology files of my ligands using external tools like PRODRG server. I tried to correct the charges in line with Dr. Justin's paper *Practical Considerations for Building GROMOS-Compatible Small-Molecule Topologies, *but seems i cannot find the way, as the system crashes down during the solvating stage with an error message;* the net charge of my structure is not an integer value. * I will be glad to get any assistance. Thank you. -- *MUSYOKA THOMMAS MUTEMI Mob nos **+27844846540** B.Sc Biochemistry (Kenyatta University),MSc Pharmaceutical Science (Nagasaki University)* *PhD Student-Bioinformatics (Rhodes University) *Skype ID- MUSYOKA THOMMAS MUTEMI Alternative email - thom...@sia.co.ke * Do all the good you can, By all the means you can, In all the ways you can, In all the places you can, At all the times you can, To all the people you can, As long as ever you can. - John Wesley. * -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] GaussView 4.0 and ITP adjuster
Hmmm GaussView is a supplement to Gaussian to prepare input files and visualize some (but far not all) results. Of course, it has nothing to do with gromacs and its topologies. Or, do I misunderstand you? Dr. Vitaly V. Chaban On Sun, Sep 8, 2013 at 1:29 PM, MUSYOKA THOMMAS mutemibiochemis...@gmail.com wrote: Dear Users, I am trying to run Protein-Ligand MD simulations using GROMACS. However, i seem to be lost in building correct ligand topologies. I came across an article explaining that the above mentioned softwares can be used to build a ligand topology file that can act as a guide in allocating correct charges and charge groups. Is there anyone who have used them before? If you have, would you kindly help me in finding my way especially in generating .out files using the GaussView. Thank you. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] GaussView 4.0 and ITP adjuster
Hi Dr, Check that link and see the role of GaussView in GROMACS. Thank you. http://www.hindawi.com/journals/chem/2013/803151/ On Mon, Sep 9, 2013 at 12:46 PM, Dr. Vitaly Chaban vvcha...@gmail.comwrote: Hmmm GaussView is a supplement to Gaussian to prepare input files and visualize some (but far not all) results. Of course, it has nothing to do with gromacs and its topologies. Or, do I misunderstand you? Dr. Vitaly V. Chaban On Sun, Sep 8, 2013 at 1:29 PM, MUSYOKA THOMMAS mutemibiochemis...@gmail.com wrote: Dear Users, I am trying to run Protein-Ligand MD simulations using GROMACS. However, i seem to be lost in building correct ligand topologies. I came across an article explaining that the above mentioned softwares can be used to build a ligand topology file that can act as a guide in allocating correct charges and charge groups. Is there anyone who have used them before? If you have, would you kindly help me in finding my way especially in generating .out files using the GaussView. Thank you. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- *MUSYOKA THOMMAS MUTEMI Mob nos **+27844846540** B.Sc Biochemistry (Kenyatta University),MSc Pharmaceutical Science (Nagasaki University)* *PhD Student-Bioinformatics (Rhodes University) *Skype ID- MUSYOKA THOMMAS MUTEMI Alternative email - thom...@sia.co.ke * Do all the good you can, By all the means you can, In all the ways you can, In all the places you can, At all the times you can, To all the people you can, As long as ever you can. - John Wesley. * -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] GaussView 4.0 and ITP adjuster
First we built their 3D structures in the *.pdb format using Gauss View 4.0 and Frisch et al. [30http://www.hindawi.com/journals/chem/2013/803151/#B30] and submitted them to energy minimization with Frisch et al. [30http://www.hindawi.com/journals/chem/2013/803151/#B30] using the algorithm B3LYP/3-21G with charge chelpg, in order to generate their *.out files. What does this have to do with gromacs topologies? Dr. Vitaly V. Chaban On Mon, Sep 9, 2013 at 12:53 PM, MUSYOKA THOMMAS mutemibiochemis...@gmail.com wrote: Hi Dr, Check that link and see the role of GaussView in GROMACS. Thank you. http://www.hindawi.com/journals/chem/2013/803151/ On Mon, Sep 9, 2013 at 12:46 PM, Dr. Vitaly Chaban vvcha...@gmail.comwrote: Hmmm GaussView is a supplement to Gaussian to prepare input files and visualize some (but far not all) results. Of course, it has nothing to do with gromacs and its topologies. Or, do I misunderstand you? Dr. Vitaly V. Chaban On Sun, Sep 8, 2013 at 1:29 PM, MUSYOKA THOMMAS mutemibiochemis...@gmail.com wrote: Dear Users, I am trying to run Protein-Ligand MD simulations using GROMACS. However, i seem to be lost in building correct ligand topologies. I came across an article explaining that the above mentioned softwares can be used to build a ligand topology file that can act as a guide in allocating correct charges and charge groups. Is there anyone who have used them before? If you have, would you kindly help me in finding my way especially in generating .out files using the GaussView. Thank you. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- *MUSYOKA THOMMAS MUTEMI Mob nos **+27844846540** B.Sc Biochemistry (Kenyatta University),MSc Pharmaceutical Science (Nagasaki University)* *PhD Student-Bioinformatics (Rhodes University) *Skype ID- MUSYOKA THOMMAS MUTEMI Alternative email - thom...@sia.co.ke * Do all the good you can, By all the means you can, In all the ways you can, In all the places you can, At all the times you can, To all the people you can, As long as ever you can. - John Wesley. * -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] intermittent changes in energy drift following simulation restarts in v4.6.1
Dear All,
I've been analysing a series of long (200 ns) NVE simulations (md
integrator) on ~93'000 atom systems I ran the simulations in groups of 3
using the -multi option in gromacs v4.6.1 double precision.
Simulations were run with 1 OpenMP thread per MPI process
The simulations were restarted at regular intervals using the following
submission script:
FILE=4.6_P84_DIO_
module load fftw xe-gromacs/4.6.1
# Change to the direcotry that the job was submitted from
cd $PBS_O_WORKDIR
export NPROC=`qstat -f $PBS_JOBID | grep mppwidth | awk '{print $3}'`
export NTASK=`qstat -f $PBS_JOBID | grep mppnppn | awk '{print $3}'`
aprun -n $NPROC -N $NTASK mdrun_mpi_d -deffnm $FILE -maxh 24 -multi 3
-npme 64 -append -cpi
###
The first simulation was run with the same script except the mdrun line was
aprun -n $NPROC -N $NTASK mdrun_mpi_d -deffnm $FILE -maxh 24 -multi 3
-npme 64
###
The simulations generally ran and restarted without trouble, however, in
several simulations the energy drift changed radically following the
restart.
in one simulation the simulation ran for 50 ns (including one restart)
with a drift of -141.6 +/- 0.1 kJ mol^-1 ns^1
it was restarted then had a drift of +104 +/- 1 kJ mol^-1 ns^1 for 15 ns
then was restarted and continued with a drift of -138 +/- 0.1 kJ mol^-1
ns^1 for a further 50~ns.
The other 2 simulations running in parallel with this calculation
through the -multi option did not experience a change in gradient.
the drifts were calculated by least squares analysis of the output from
the total energy data given by
echo total | g_energy_d -f ${FILE}${i}.edr -o total_${FILE}${i}.xvg
-xvg none
The simulation writes to the edr every 20 ps and the transition is
masked by the expected oscillations in energy due to the integrator on a
2~ns interval but the change in drift is clear when looking at a 4~ns
range centred on the restart.
The hardware used was of the same specification for all jobs (27 cray
XE6 nodes (9 nodes per simulation), 32 mpi processes per node)
The simulations use the verlet cut-off scheme
there are H-bond constraints enforced using lincs (order 6, iterations 2)
I can't think what would cause this change in the drift during a
restart. However, I have seen it in simulations run on both an AMD
system (cray XE6, AVX-FMA) and an intel system (SGI-ice, SSE4.1).
I have some data generated using the same procedure using v4.5.5 and
v4.5.7 (different cut-off scheme) and the restarts in that system have
not caused any appreciable changes in the simulation.
Unfortunately I didn't save the checkpoint files used for the restart (I
will in the future). I'm going to try building a new input file from
just before the restart using the trr trajectory data.
Does anyone have any ideas of what might have caused this?
Has anyone seen similar effects?
Thanks,
Richard
--
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Re: [gmx-users] intermittent changes in energy drift following simulation restarts in v4.6.1
Sounds worrying :-( Thanks for the detailed report and
trouble-shooting! So far, I can't think of a reason for it.
A couple of suggestions:
* try again with 4.6.3 (at least while trouble-shooting) in case its a fixed bug
* post a representative .mdp file
* is there anything out of the ordinary in the topology?
* if the problem is restart-related and shows up in the drift quickly,
then you can probably find a reproducible case via a job that does
lots of short-interval restarts and saves all the intermediate files -
a (set of) inputs that can reproduce the problem sounds like what we'd
need to diagnose and/or fix anything
* does it happen in a non-multi simulation? (or more particularly,
what are you doing with -multi?)
* check .log files for warnings, and that there are none being
suppressed at the grompp stage
* see if the group cut-off scheme in 4.6.x shows the same problem
Mark
On Mon, Sep 9, 2013 at 4:08 PM, Richard Broadbent
richard.broadben...@imperial.ac.uk wrote:
Dear All,
I've been analysing a series of long (200 ns) NVE simulations (md
integrator) on ~93'000 atom systems I ran the simulations in groups of 3
using the -multi option in gromacs v4.6.1 double precision.
Simulations were run with 1 OpenMP thread per MPI process
The simulations were restarted at regular intervals using the following
submission script:
FILE=4.6_P84_DIO_
module load fftw xe-gromacs/4.6.1
# Change to the direcotry that the job was submitted from
cd $PBS_O_WORKDIR
export NPROC=`qstat -f $PBS_JOBID | grep mppwidth | awk '{print $3}'`
export NTASK=`qstat -f $PBS_JOBID | grep mppnppn | awk '{print $3}'`
aprun -n $NPROC -N $NTASK mdrun_mpi_d -deffnm $FILE -maxh 24 -multi 3
-npme 64 -append -cpi
###
The first simulation was run with the same script except the mdrun line was
aprun -n $NPROC -N $NTASK mdrun_mpi_d -deffnm $FILE -maxh 24 -multi 3
-npme 64
###
The simulations generally ran and restarted without trouble, however, in
several simulations the energy drift changed radically following the
restart.
in one simulation the simulation ran for 50 ns (including one restart) with
a drift of -141.6 +/- 0.1 kJ mol^-1 ns^1
it was restarted then had a drift of +104 +/- 1 kJ mol^-1 ns^1 for 15 ns
then was restarted and continued with a drift of -138 +/- 0.1 kJ mol^-1 ns^1
for a further 50~ns.
The other 2 simulations running in parallel with this calculation through
the -multi option did not experience a change in gradient.
the drifts were calculated by least squares analysis of the output from the
total energy data given by
echo total | g_energy_d -f ${FILE}${i}.edr -o total_${FILE}${i}.xvg -xvg
none
The simulation writes to the edr every 20 ps and the transition is masked by
the expected oscillations in energy due to the integrator on a 2~ns interval
but the change in drift is clear when looking at a 4~ns range centred on the
restart.
The hardware used was of the same specification for all jobs (27 cray XE6
nodes (9 nodes per simulation), 32 mpi processes per node)
The simulations use the verlet cut-off scheme
there are H-bond constraints enforced using lincs (order 6, iterations 2)
I can't think what would cause this change in the drift during a restart.
However, I have seen it in simulations run on both an AMD system (cray XE6,
AVX-FMA) and an intel system (SGI-ice, SSE4.1).
I have some data generated using the same procedure using v4.5.5 and v4.5.7
(different cut-off scheme) and the restarts in that system have not caused
any appreciable changes in the simulation.
Unfortunately I didn't save the checkpoint files used for the restart (I
will in the future). I'm going to try building a new input file from just
before the restart using the trr trajectory data.
Does anyone have any ideas of what might have caused this?
Has anyone seen similar effects?
Thanks,
Richard
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the www
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--
gmx-users mailing listgmx-users@gromacs.org
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* Please search the archive at
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Re: [gmx-users] intermittent changes in energy drift following simulation restarts in v4.6.1
Hi Mark,
Thanks for the quick response,
On 09/09/13 15:45, Mark Abraham wrote:
Sounds worrying :-( Thanks for the detailed report and
trouble-shooting! So far, I can't think of a reason for it.
A couple of suggestions:
* try again with 4.6.3 (at least while trouble-shooting) in case its a fixed bug
I'll test that side by side with 4.6.1 that way we can have both for
comparison
* post a representative .mdp file
its below this message the production run is built using tpbconv -extend
on the .tpr built from that .mdp.
* is there anything out of the ordinary in the topology?
I built the residues myself but they're just standard polymer monomer
units nothing out of the ordinary.
* if the problem is restart-related and shows up in the drift quickly,
then you can probably find a reproducible case via a job that does
lots of short-interval restarts and saves all the intermediate files -
a (set of) inputs that can reproduce the problem sounds like what we'd
need to diagnose and/or fix anything
I'm already starting to build them will be testing them tomorrow
* does it happen in a non-multi simulation? (or more particularly,
what are you doing with -multi?)
The -multi was used to move the job into a faster queue I've seen it in
non -multi jobs
* check .log files for warnings, and that there are none being
suppressed at the grompp stage
There are no errors at grompp stage
I haven't identified any warnings in the mdrun logs but I'm going to
have a another look before I'm 100% certain that there aren't any in
there but I couldn't see any on a first look through
* see if the group cut-off scheme in 4.6.x shows the same problem
Will do
Mark
Thanks,
Richard
integrator = md
bd_fric = 0
dt = 0.002
nsteps = 250
comm_mode = linear
nstxout = 10
nstvout = 10
nstfout = 0
xtc_grps = P84
nstxtcout = 5
nstlog = 10
nstenergy = 5
pbc = xyz
periodic_molecules = no
ns_type = grid
nstlist = 10
rlist = 1.25
optimize_fft = yes
fourier_nx = 128
fourier_ny = 128
fourier_nz = 128
pme_order = 4
epsilon_r = 1.0
coulombtype = pme
coulomb-modifier = Potential-shift-Verlet
rcoulomb = 1.2
vdwtype = cut-off
vdw-modifier = Potential-shift-Verlet
rvdw = 1.20
DispCorr = EnerPres
tcoupl = no
nsttcouple = 5
pcoupl = no
constraints = h-bonds
lincs_order = 6
lincs_iter = 2
cutoff-scheme = Verlet
verlet-buffer-drift = -1
On Mon, Sep 9, 2013 at 4:08 PM, Richard Broadbent
richard.broadben...@imperial.ac.uk wrote:
Dear All,
I've been analysing a series of long (200 ns) NVE simulations (md
integrator) on ~93'000 atom systems I ran the simulations in groups of 3
using the -multi option in gromacs v4.6.1 double precision.
Simulations were run with 1 OpenMP thread per MPI process
The simulations were restarted at regular intervals using the following
submission script:
FILE=4.6_P84_DIO_
module load fftw xe-gromacs/4.6.1
# Change to the direcotry that the job was submitted from
cd $PBS_O_WORKDIR
export NPROC=`qstat -f $PBS_JOBID | grep mppwidth | awk '{print $3}'`
export NTASK=`qstat -f $PBS_JOBID | grep mppnppn | awk '{print $3}'`
aprun -n $NPROC -N $NTASK mdrun_mpi_d -deffnm $FILE -maxh 24 -multi 3
-npme 64 -append -cpi
###
The first simulation was run with the same script except the mdrun line was
aprun -n $NPROC -N $NTASK mdrun_mpi_d -deffnm $FILE -maxh 24 -multi 3
-npme 64
###
The simulations generally ran and restarted without trouble, however, in
several simulations the energy drift changed radically following the
restart.
in one simulation the simulation ran for 50 ns (including one restart) with
a drift of -141.6 +/- 0.1 kJ mol^-1 ns^1
it was restarted then had a drift of +104 +/- 1 kJ mol^-1 ns^1 for 15 ns
then was restarted and continued with a drift of -138 +/- 0.1 kJ mol^-1 ns^1
for a further 50~ns.
The other 2 simulations running in parallel with this calculation through
the -multi option did not experience a change in gradient.
the drifts were calculated by least squares analysis of the output from the
total energy data given by
echo total | g_energy_d -f ${FILE}${i}.edr -o total_${FILE}${i}.xvg -xvg
none
The simulation writes to the edr every 20 ps and the transition is masked by
the expected oscillations in energy due to the integrator on a 2~ns interval
but the change in drift is clear when looking at a 4~ns range centred on the
restart.
The hardware used was of the same specification for all jobs (27 cray XE6
nodes (9 nodes per simulation), 32 mpi processes per node)
The simulations use the verlet cut-off scheme
there are H-bond constraints enforced using lincs (order 6, iterations 2)
I can't think what would cause this change in the drift during a restart.
However, I have seen it in simulations run on both an AMD system (cray XE6,
AVX-FMA) and an intel system (SGI-ice, SSE4.1).
I have some data generated using the same procedure using v4.5.5 and v4.5.7
(different cut-off scheme) and
RE: [gmx-users] g_current
Hi, as I just recently left the university and started to work in industry, there are currently a lot of things to be done. However, I will still try to contribute to GROMACS as good as possible. Next week there will be some time left in the evening and I will report back ASAP. /Flo -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of Nilesh Dhumal Sent: Sunday, September 08, 2013 11:55 PM To: Discussion list for GROMACS users Subject: RE: [gmx-users] g_current Did you get chance to take look at the g_current? why it is -inf (infinity) at the end with -mc option (mc.xvg). -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of Nilesh Dhumal Sent: Tuesday, July 09, 2013 5:06 AM To: Discussion list for GROMACS users Subject: RE: [gmx-users] g_current Thanks for reply. Still I have a question why it is -inf (infinity) at the end. This is a good question. At the moment, the only thing I can imagine is a faulty normalization, because the value of the integral at t=0 equals always zero. However, if you integrate the first row with another tool, such as g_analyze for example, the same values as in the second row show appear. As soon as I have some time left, I will take a look at the code and report back. /Flo Nilesh Hi, I would say the problem is too less statistics. In the paper where the tool was introduced, a simulation of 100ns has been performed in order to achieved sufficient sampling. The order of magnitude is given due to the units. Simulate for a longer time to get rid of the noise. Calculating these kind of correlations functions is really not a simple task. Schroeder et al. have published an article about fitting of dielectric spectra for ionic liquids, where this problem is discussed in detail. Cheers, Flo -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of Nilesh Dhumal Sent: Monday, July 08, 2013 10:32 PM To: gmx-users@gromacs.org Subject: [gmx-users] g_current Hello, I am calculating the correlation of rotational and translation dipole moment of ionic liquids. I run the 1 ns simulation and saved the trajectory at 1 fs. g_current -f md.trr -s md.tpr -n index.ndx -mc I selected system group. Here I pasted the initial j(t) vales and the final value is infinity. # This file was created Sun Jul 7 20:51:59 2013 # by the following command: # g_current -f md.trr -s md.tpr -e 10.0 -mc # # g_current is part of G R O M A C S: # # Gallium Rubidium Oxygen Manganese Argon Carbon Silicon # @title M\sD\N - current autocorrelation function @xaxis label Time (ps) @yaxis label M\sD\N (0)\c7\CJ(t) (e nm/ps)\S2 @TYPE xy # time M_D(0) J(t) acf Integral acf 0.000 -5.20584e-15 0 0.001 -6.97466e-15-1.42702e-17 0.002 -6.97511e-15-5.25081e-17 0.003 -6.97474e-15-9.07484e-17 0.004 -6.97391e-15-1.28987e-16 Why final value is infinity? If I do autocorrelation function of these values, I get all values 0. Why J(t)values are in range of e-15? Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to
Re: [gmx-users] intermittent changes in energy drift following simulation restarts in v4.6.1
No obvious problems. Please open an issue at redmine.gromacs.org when you
have something reproducible, but don't hurry, nobody's likely to have time
to check it out for a week or two.
Cheers,
Mark
On Sep 9, 2013 5:11 PM, Richard Broadbent
richard.broadben...@imperial.ac.uk wrote:
Hi Mark,
Thanks for the quick response,
On 09/09/13 15:45, Mark Abraham wrote:
Sounds worrying :-( Thanks for the detailed report and
trouble-shooting! So far, I can't think of a reason for it.
A couple of suggestions:
* try again with 4.6.3 (at least while trouble-shooting) in case its a
fixed bug
I'll test that side by side with 4.6.1 that way we can have both for
comparison
* post a representative .mdp file
its below this message the production run is built using tpbconv -extend
on the .tpr built from that .mdp.
* is there anything out of the ordinary in the topology?
I built the residues myself but they're just standard polymer monomer
units nothing out of the ordinary.
* if the problem is restart-related and shows up in the drift quickly,
then you can probably find a reproducible case via a job that does
lots of short-interval restarts and saves all the intermediate files -
a (set of) inputs that can reproduce the problem sounds like what we'd
need to diagnose and/or fix anything
I'm already starting to build them will be testing them tomorrow
* does it happen in a non-multi simulation? (or more particularly,
what are you doing with -multi?)
The -multi was used to move the job into a faster queue I've seen it in
non -multi jobs
* check .log files for warnings, and that there are none being
suppressed at the grompp stage
There are no errors at grompp stage
I haven't identified any warnings in the mdrun logs but I'm going to have
a another look before I'm 100% certain that there aren't any in there but I
couldn't see any on a first look through
* see if the group cut-off scheme in 4.6.x shows the same problem
Will do
Mark
Thanks,
Richard
integrator = md
bd_fric = 0
dt = 0.002
nsteps = 250
comm_mode = linear
nstxout = 10
nstvout = 10
nstfout = 0
xtc_grps = P84
nstxtcout = 5
nstlog = 10
nstenergy = 5
pbc = xyz
periodic_molecules = no
ns_type = grid
nstlist = 10
rlist = 1.25
optimize_fft = yes
fourier_nx = 128
fourier_ny = 128
fourier_nz = 128
pme_order = 4
epsilon_r = 1.0
coulombtype = pme
coulomb-modifier = Potential-shift-Verlet
rcoulomb = 1.2
vdwtype = cut-off
vdw-modifier = Potential-shift-Verlet
rvdw = 1.20
DispCorr = EnerPres
tcoupl = no
nsttcouple = 5
pcoupl = no
constraints = h-bonds
lincs_order = 6
lincs_iter = 2
cutoff-scheme = Verlet
verlet-buffer-drift = -1
On Mon, Sep 9, 2013 at 4:08 PM, Richard Broadbent
richard.broadbent09@imperial.**ac.ukrichard.broadben...@imperial.ac.uk
wrote:
Dear All,
I've been analysing a series of long (200 ns) NVE simulations (md
integrator) on ~93'000 atom systems I ran the simulations in groups of 3
using the -multi option in gromacs v4.6.1 double precision.
Simulations were run with 1 OpenMP thread per MPI process
The simulations were restarted at regular intervals using the following
submission script:
FILE=4.6_P84_DIO_
module load fftw xe-gromacs/4.6.1
# Change to the direcotry that the job was submitted from
cd $PBS_O_WORKDIR
export NPROC=`qstat -f $PBS_JOBID | grep mppwidth | awk '{print $3}'`
export NTASK=`qstat -f $PBS_JOBID | grep mppnppn | awk '{print $3}'`
aprun -n $NPROC -N $NTASK mdrun_mpi_d -deffnm $FILE -maxh 24 -multi 3
-npme 64 -append -cpi
###
The first simulation was run with the same script except the mdrun line
was
aprun -n $NPROC -N $NTASK mdrun_mpi_d -deffnm $FILE -maxh 24 -multi 3
-npme 64
###
The simulations generally ran and restarted without trouble, however, in
several simulations the energy drift changed radically following the
restart.
in one simulation the simulation ran for 50 ns (including one restart)
with
a drift of -141.6 +/- 0.1 kJ mol^-1 ns^1
it was restarted then had a drift of +104 +/- 1 kJ mol^-1 ns^1 for 15 ns
then was restarted and continued with a drift of -138 +/- 0.1 kJ mol^-1
ns^1
for a further 50~ns.
The other 2 simulations running in parallel with this calculation through
the -multi option did not experience a change in gradient.
the drifts were calculated by least squares analysis of the output from
the
total energy data given by
echo total | g_energy_d -f ${FILE}${i}.edr -o total_${FILE}${i}.xvg
-xvg
none
The simulation writes to the edr every 20 ps and the transition is
masked by
the expected oscillations in energy due to the integrator on a 2~ns
interval
but the change in drift is clear when looking at a 4~ns range centred on
the
restart.
The hardware used was of the same specification for all jobs (27 cray XE6
nodes (9 nodes per simulation), 32 mpi processes
Re: [gmx-users] NMR restrained MD
Ok..I got it Thanks Justin... --Rama On Mon, Sep 9, 2013 at 1:49 PM, Rama Krishna Koppisetti ramkishn...@gmail.com wrote: Hi Justin , I prepared .rtp files for lipid. what is the exact command to merge two chains in gromacs. On Fri, Sep 6, 2013 at 4:37 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/6/13 5:35 PM, Rama Krishna Koppisetti wrote: H i Justin, Thanks for your reply. How to do that? If .rtp entries exist for your lipid with the force field, it's simply a matter of pdb2gmx -merge, choosing which chains should be written as a single [moleculetype]. If the lipids are not described by .rtp entries, you either have to write one or modify the topology by hand (ugh) or with some script. -Justin On Fri, Sep 6, 2013 at 4:27 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/6/13 5:23 PM, Rama wrote: Hi, I'm doing NMR restrained MD simulation for protein-Bilayer system to satisfy NMR experimental data. Without restraints there is no problem, but if I include distance restraints in topology file, getting fatal error: the lipid atom index # was not recognized by using this command: g_grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o md.tpr -maxwarn 5 even in index file protein_DMPC atoms index is there continuously. Any one have suggestions to overcome this fatal error. Thanks / [ file beta_disres.itp, line 4 ]: Atom index (2679) in distance_restraints out of bounds (1-2513)./ Just like position restraints, distance restraints only work within a [moleculetype]. Thus you're probably trying to restrain atoms between [moleculetype] directives, which does not work. You could theoretically make a merged [moleculetype] of whatever species need to be restrained, but that may take a bit of effort depending on what is being restrained. -Justin md.mdp file: title = protein-bilayer complex define = -DDISRES ; NMR Distance restraints ; Run parameters integrator = md; leap-frog integrator nsteps = 250 ; dt = 0.002 ; 2 fs ; Output control nstxout = 5000 ; save coordinates every 5 ps nstvout = 5000 ; save velocities every 5 ps nstxtcout = 5000 ; xtc compressed trajectory output every 5 ps nstenergy = 5000 ; save energies every 5 ps nstlog = 5000 ; update log file every 5 ps ; Bond parameters continuation= yes ; Restarting after NPT constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Distance restraints parameters disre = simple; simple (per-molecule) disre_fc= 1000 ; force constant for distance restraints ; Neighborsearching ns_type = grid ; search neighboring grid cels nstlist = 5 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rcoulomb= 1.2 ; short-range electrostatic cutoff (in nm) rvdw= 1.2 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = Nose-Hoover ; More accurate thermostat tc-grps = Protein non-protein non-protein ; three coupling groups - more accurate tau_t = 0.5 0.5 0.5 ; time constant, in ps ref_t = 303 303 303 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = semiisotropic ; uniform scaling of x-y box vectors, independent z tau_p = 2.0 ; time constant, in ps ref_p = 1.0 1.0 ; reference pressure, x-y, z (in bar) compressibility = 4.5e-54.5e-5 ; isothermal compressibility, bar^-1 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no; Velocity generation is off ; COM motion removal ; These options remove motion of the protein/bilayer relative to the solvent/ions nstcomm = 1 comm-mode = Linear comm-grps = protein non-protein topology file: ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ;
Re: [gmx-users] NMR restrained MD
Hi Justin , I prepared .rtp files for lipid. what is the exact command to merge two chains in gromacs. On Fri, Sep 6, 2013 at 4:37 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/6/13 5:35 PM, Rama Krishna Koppisetti wrote: H i Justin, Thanks for your reply. How to do that? If .rtp entries exist for your lipid with the force field, it's simply a matter of pdb2gmx -merge, choosing which chains should be written as a single [moleculetype]. If the lipids are not described by .rtp entries, you either have to write one or modify the topology by hand (ugh) or with some script. -Justin On Fri, Sep 6, 2013 at 4:27 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/6/13 5:23 PM, Rama wrote: Hi, I'm doing NMR restrained MD simulation for protein-Bilayer system to satisfy NMR experimental data. Without restraints there is no problem, but if I include distance restraints in topology file, getting fatal error: the lipid atom index # was not recognized by using this command: g_grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o md.tpr -maxwarn 5 even in index file protein_DMPC atoms index is there continuously. Any one have suggestions to overcome this fatal error. Thanks / [ file beta_disres.itp, line 4 ]: Atom index (2679) in distance_restraints out of bounds (1-2513)./ Just like position restraints, distance restraints only work within a [moleculetype]. Thus you're probably trying to restrain atoms between [moleculetype] directives, which does not work. You could theoretically make a merged [moleculetype] of whatever species need to be restrained, but that may take a bit of effort depending on what is being restrained. -Justin md.mdp file: title = protein-bilayer complex define = -DDISRES ; NMR Distance restraints ; Run parameters integrator = md; leap-frog integrator nsteps = 250 ; dt = 0.002 ; 2 fs ; Output control nstxout = 5000 ; save coordinates every 5 ps nstvout = 5000 ; save velocities every 5 ps nstxtcout = 5000 ; xtc compressed trajectory output every 5 ps nstenergy = 5000 ; save energies every 5 ps nstlog = 5000 ; update log file every 5 ps ; Bond parameters continuation= yes ; Restarting after NPT constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Distance restraints parameters disre = simple; simple (per-molecule) disre_fc= 1000 ; force constant for distance restraints ; Neighborsearching ns_type = grid ; search neighboring grid cels nstlist = 5 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rcoulomb= 1.2 ; short-range electrostatic cutoff (in nm) rvdw= 1.2 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = Nose-Hoover ; More accurate thermostat tc-grps = Protein non-protein non-protein ; three coupling groups - more accurate tau_t = 0.5 0.5 0.5 ; time constant, in ps ref_t = 303 303 303 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = semiisotropic ; uniform scaling of x-y box vectors, independent z tau_p = 2.0 ; time constant, in ps ref_p = 1.0 1.0 ; reference pressure, x-y, z (in bar) compressibility = 4.5e-54.5e-5 ; isothermal compressibility, bar^-1 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no; Velocity generation is off ; COM motion removal ; These options remove motion of the protein/bilayer relative to the solvent/ions nstcomm = 1 comm-mode = Linear comm-grps = protein non-protein topology file: ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Include Distance restraints file #ifdef DISRES #include beta_disres.itp #endif ; Strong position restraints for InflateGRO #ifdef
[gmx-users] segfault on Gromacs 4.6.3 (cuda)
Dear GMX users, I recently compiled Gromacs 4.6.3 with CUDA (Intel compiler 11.x, SSE2, and CUDA SDK 5.0.35). I was doing a test run with simply 'mdrun -deffnm eq2_npt_verlet' (letting mdrun figure out what to use). I received the error telling me my graphics driver was older than the CUDA SDK, and regular CPU code would be used instead. Then, it crashed with Segmentation Fault. The code runs properly on another node where the graphics driver is more up to date. I wonder if the crashing is somewhat expected, and therefore I should prepare different binaries based on the capabilities of different nodes. Thanks. Best regards, -- Guanglei Cui -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] segfault on Gromacs 4.6.3 (cuda)
HI, First of all, icc 11 is not well tested and there have been reports about it compiling broken code. This could explain the crash, but you'd need to do a bit more testing to confirm. Regading the GPU detection error, if you use a driver which is incompatible with the CUDA runtime (at least as high API version, see the mdrun log header's last two lines) and at the moment, some of such cases are not detected particularly gracefully. A few things to try: - use gcc, 4.7 is as fast or faster than any icc; - run with the -nb cpu option; does it still crash? - run with GPU detection completely disabled* - run the regressiontests; try using CPUs only* *You can set the GMX_DISABLE_GPU_DETECTION environment variable to completely disable the GPU detection. Cheers, -- Szilárd On Mon, Sep 9, 2013 at 9:52 PM, Guanglei Cui amber.mail.arch...@gmail.com wrote: Dear GMX users, I recently compiled Gromacs 4.6.3 with CUDA (Intel compiler 11.x, SSE2, and CUDA SDK 5.0.35). I was doing a test run with simply 'mdrun -deffnm eq2_npt_verlet' (letting mdrun figure out what to use). I received the error telling me my graphics driver was older than the CUDA SDK, and regular CPU code would be used instead. Then, it crashed with Segmentation Fault. The code runs properly on another node where the graphics driver is more up to date. I wonder if the crashing is somewhat expected, and therefore I should prepare different binaries based on the capabilities of different nodes. Thanks. Best regards, -- Guanglei Cui -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] NMR restrained MD
Hi Justin, I included 1 DMPC molecule parameters in the file should I need to include 128 molecules parameters in the file .rtp. Thanks --Rama On Mon, Sep 9, 2013 at 4:43 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/9/13 5:37 PM, Rama Krishna Koppisetti wrote: Hi Justin, I merge two molecules as a single molecule type. Now I'm trying to do energy minimization of the system, getting errors like Fatal error: [file topol.top, line 55130]: No default Proper Dih. types Any idea for this type of errors. The force field does not have parameters for whatever dihedral is listed on line 55130 in the topology. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] NMR restrained MD
Hi Justin, I merge two molecules as a single molecule type. Now I'm trying to do energy minimization of the system, getting errors like Fatal error: [file topol.top, line 55130]: No default Proper Dih. types Any idea for this type of errors. Thanks --Rama On Mon, Sep 9, 2013 at 1:57 PM, Rama Krishna Koppisetti ramkishn...@gmail.com wrote: Ok..I got it Thanks Justin... --Rama On Mon, Sep 9, 2013 at 1:49 PM, Rama Krishna Koppisetti ramkishn...@gmail.com wrote: Hi Justin , I prepared .rtp files for lipid. what is the exact command to merge two chains in gromacs. On Fri, Sep 6, 2013 at 4:37 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/6/13 5:35 PM, Rama Krishna Koppisetti wrote: H i Justin, Thanks for your reply. How to do that? If .rtp entries exist for your lipid with the force field, it's simply a matter of pdb2gmx -merge, choosing which chains should be written as a single [moleculetype]. If the lipids are not described by .rtp entries, you either have to write one or modify the topology by hand (ugh) or with some script. -Justin On Fri, Sep 6, 2013 at 4:27 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/6/13 5:23 PM, Rama wrote: Hi, I'm doing NMR restrained MD simulation for protein-Bilayer system to satisfy NMR experimental data. Without restraints there is no problem, but if I include distance restraints in topology file, getting fatal error: the lipid atom index # was not recognized by using this command: g_grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o md.tpr -maxwarn 5 even in index file protein_DMPC atoms index is there continuously. Any one have suggestions to overcome this fatal error. Thanks / [ file beta_disres.itp, line 4 ]: Atom index (2679) in distance_restraints out of bounds (1-2513)./ Just like position restraints, distance restraints only work within a [moleculetype]. Thus you're probably trying to restrain atoms between [moleculetype] directives, which does not work. You could theoretically make a merged [moleculetype] of whatever species need to be restrained, but that may take a bit of effort depending on what is being restrained. -Justin md.mdp file: title = protein-bilayer complex define = -DDISRES ; NMR Distance restraints ; Run parameters integrator = md; leap-frog integrator nsteps = 250 ; dt = 0.002 ; 2 fs ; Output control nstxout = 5000 ; save coordinates every 5 ps nstvout = 5000 ; save velocities every 5 ps nstxtcout = 5000 ; xtc compressed trajectory output every 5 ps nstenergy = 5000 ; save energies every 5 ps nstlog = 5000 ; update log file every 5 ps ; Bond parameters continuation= yes ; Restarting after NPT constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Distance restraints parameters disre = simple; simple (per-molecule) disre_fc= 1000 ; force constant for distance restraints ; Neighborsearching ns_type = grid ; search neighboring grid cels nstlist = 5 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rcoulomb= 1.2 ; short-range electrostatic cutoff (in nm) rvdw= 1.2 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = Nose-Hoover ; More accurate thermostat tc-grps = Protein non-protein non-protein ; three coupling groups - more accurate tau_t = 0.5 0.5 0.5 ; time constant, in ps ref_t = 303 303 303 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = semiisotropic ; uniform scaling of x-y box vectors, independent z tau_p = 2.0 ; time constant, in ps ref_p = 1.0 1.0 ; reference pressure, x-y, z (in bar) compressibility = 4.5e-54.5e-5 ; isothermal compressibility, bar^-1 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity
Re: [gmx-users] NMR restrained MD
On 9/9/13 6:11 PM, Rama Krishna Koppisetti wrote: Hi Justin, I included 1 DMPC molecule parameters in the file should I need to include 128 molecules parameters in the file .rtp. No. Residue definitions are used any time they are encountered in the coordinate file. There is no need for such redundancy at the force field level. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] NMR restrained MD
On 9/9/13 5:37 PM, Rama Krishna Koppisetti wrote: Hi Justin, I merge two molecules as a single molecule type. Now I'm trying to do energy minimization of the system, getting errors like Fatal error: [file topol.top, line 55130]: No default Proper Dih. types Any idea for this type of errors. The force field does not have parameters for whatever dihedral is listed on line 55130 in the topology. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] segfault on Gromacs 4.6.3 (cuda)
Hi Szilard, Thanks again for getting back. You may remember the previous thread I started on regression test failure with icc 11.x compiled binary. Falling back to SSE2 is my solution, and binaries compiled this way are able to pass all regression tests, including the one with GPU switched on. However, it is not clear to me if the GPU part is specifically tested in the regression. As I was trying to explain in the original email, the binary works fine on a node with proper graphics driver, but crashes on a node where the graphics driver is older than the CUDA SDK used in compilation. I think updating the driver may potentially enable the GPU part. Pure CPU calculation with the same binary seems not working. It is not clear to me if this is caused by the compiler. It's not really simple to update the gcc to 4.7 or greater since we use CentOS 5.x in the company. Even CentOS 6.x uses gcc 4.4.x as default. I've just tested the code with -nb cpu. It still crashes. The binary compiled without GPU works as expected and passed all regression tests. For now, I can keep separate binaries for GPU and CPU applications before I can get gcc 4.7 or greater installed. Best regards, Guanglei On Mon, Sep 9, 2013 at 4:35 PM, Szilárd Páll szilard.p...@cbr.su.se wrote: HI, First of all, icc 11 is not well tested and there have been reports about it compiling broken code. This could explain the crash, but you'd need to do a bit more testing to confirm. Regading the GPU detection error, if you use a driver which is incompatible with the CUDA runtime (at least as high API version, see the mdrun log header's last two lines) and at the moment, some of such cases are not detected particularly gracefully. A few things to try: - use gcc, 4.7 is as fast or faster than any icc; - run with the -nb cpu option; does it still crash? - run with GPU detection completely disabled* - run the regressiontests; try using CPUs only* *You can set the GMX_DISABLE_GPU_DETECTION environment variable to completely disable the GPU detection. Cheers, -- Szilárd On Mon, Sep 9, 2013 at 9:52 PM, Guanglei Cui amber.mail.arch...@gmail.com wrote: Dear GMX users, I recently compiled Gromacs 4.6.3 with CUDA (Intel compiler 11.x, SSE2, and CUDA SDK 5.0.35). I was doing a test run with simply 'mdrun -deffnm eq2_npt_verlet' (letting mdrun figure out what to use). I received the error telling me my graphics driver was older than the CUDA SDK, and regular CPU code would be used instead. Then, it crashed with Segmentation Fault. The code runs properly on another node where the graphics driver is more up to date. I wonder if the crashing is somewhat expected, and therefore I should prepare different binaries based on the capabilities of different nodes. Thanks. Best regards, -- Guanglei Cui -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Guanglei Cui -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
