[gmx-users] ligand dissociation in gromacs

[venkat]

Sir,
  i need to study Crystal complex structure (protein and ligand)
ligand dissociation by using md methods.  Is there any way perform in
gromacs like RAMD
if its there means kindly provide tutorial for that it will helpful for me.

Thank You.

Sincerely
S.venkatesh
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[gmx-users] How to perform RAMD in gromacs -reg

[venkat]

Dear Gromacs users/developers,
To study ligand disassociation
from binding pocket of protein, how do implement in RAMD in gromacs
searched for tutorial, am not getting any relevant, could you don't mind
can share that info/procedure proceed further.
Thank you

Sincerely
s.venkatesh
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[gmx-users] mdrun -rerun

[venkat]

Hi,
For my work, I did  md simulations (200ns)  by setting with
0.5 ns xtc and 0.5  ns trr files (interval used to save the coordinates).
But now  I require 4000 frame for 200 ns MD simulations trajectory  (25000
steps, 500 ps)  is that possible to get from using "*-rerun*"  option or
need to run freshly ?.

Thanks in Advance
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[gmx-users] covar warning

[venkat]

Hi,
For PCA analysis  i tried to run covar tool for my task, i got following
warning ​
"​
WARNING: there are fewer frames in your trajectory than there are
​ ​
​
degrees of freedom in your system. Only generating the first
​ ​
400 out of 3564 eigenvectors and eigenvalues.
​"​
Why it generating 400  out of 3564 eigevectors,  How rectify this warning ?
kindly help .  (Command used : gmx_mpi covar -s prot_only-apo.pdb -f
PROTEIN.xtc -v eigenvect.trr -xpma covara.xpm)

Thank you
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[gmx-users] there are fewer frames in your trajectory than there are degrees of freedom in your system.

[venkat]

Dear gromacs users,
i tried to analysis trajectory using covar
command (gmx_mpi covar -s *prot_only-apo.pdb *-f *PROTEIN.xtc* -v
eigenvect.trr -xpma covara.xpm)
 i got following warning
*WARNING: there are fewer frames in your trajectory than there are degrees
of freedom in your system. Only generating the first 400 out of 3564
eigenvectors and eigenvalues.*

 kindly provide suggestions weather can i ignore above mentioned warning or
not

thank you
venkat
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[gmx-users] Covarience matrix eps file atom interval set -reg

[venkat]

 Hi,
 I did  covar analysis  with option  xpma  for  1188  c-alpha atoms ,
followed by xpma file converted using xpm2ps , i got following image , here
need is to set or interval of  200 atoms. How can I do this ?   (i tried
with -do flag for modified .m2p file , not working for me )

kindly provide suggestion

thanks you in advance

click view the image

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[gmx-users] paralllelized gromacs run creating same file in many times -reg

[venkat]

Hello,
 I installed Gromacs-2016.4 using (compiled using:
intel-parallel-studio-2016, gcc4.8.5),
I tried gromacs run parallelized on 32 cores, i seen  multiple instances of
mdrun, each one using one MPI process,
also many gromacs header in the log file, in directory  log, ene, traj_comp
files are creating multiple times

so, I expecting your suggestions to rectify this issue.

thank you

*FOR JOB SUBMISSION FOLLOWED SCRIPT USED *
#! /bin/bash
##PBS -l walltime=48:00:00
#PBS -N gromacs
#PBS -q workq
#PBS -l select=2:ncpus=16:mpiprocs=16
#PBS -S /bin/csh
#PBS -V
# Go to the directory from which you submitted the job

cd $PBS_O_WORKDIR

module purge
module load gcc4.8.5
module load gsl-2.0
module load intel-parallel-studio-2016
module load gromacs-2016.4_Plumbedpatch
module load openmpi-3.0
module load plumed-2.4

export MPI_DEBUG=all
export MPI_IB_RAILS=2
export MPI_DSM_DISTRIBUTE=1
export MPI_VERBOSE=1
export MPI_BUFS_THRESHOLD=1
export MPI_BUFS_PER_PROC=1024
export OMP_NUM_THREADS=1

mpirun -np 32 /app/gromacs-2016.4_plumbSWpatch/bin/gmx_mpi mdrun -v -s
topol -nsteps 500 &> 6ter.log


*##DIRECTORY  *
*ls -lrt *

  Feb  1 10:52 #ener.edr.51#
Feb  1 10:52 #ener.edr.50#
Feb  1 10:52 #ener.edr.49#
Feb  1 10:52 #ener.edr.48#
Feb  1 10:52 #ener.edr.47#
Feb  1 10:52 #ener.edr.46#
Feb  1 10:52 #ener.edr.45#
Feb  1 10:52 #ener.edr.44#
Feb  1 10:52 #ener.edr.43#
Feb  1 10:52 #ener.edr.42#
Feb  1 10:52 #ener.edr.41#
Feb  1 10:52 #ener.edr.40#
Feb  1 10:52 #ener.edr.39#
Feb  1 10:52 #ener.edr.38#
Feb  1 10:52 #ener.edr.37#
Feb  1 10:52 #ener.edr.36#
Feb  1 10:52 #ener.edr.35#
Feb  1 10:52 #ener.edr.34#
Feb  1 10:52 #ener.edr.33#
Feb  1 10:52 #ener.edr.32#
Feb  1 10:52 ener.edr
Feb  1 10:52 #traj_comp.xtc.57#
Feb  1 10:52 #traj_comp.xtc.56#
Feb  1 10:52 #traj_comp.xtc.55#
Feb  1 10:52 #traj_comp.xtc.54#
Feb  1 10:52 #traj_comp.xtc.53#
Feb  1 10:52 #traj_comp.xtc.52#
Feb  1 10:52 #traj_comp.xtc.51#
Feb  1 10:52 #traj_comp.xtc.50#
Feb  1 10:52 #traj_comp.xtc.49#
Feb  1 10:52 #traj_comp.xtc.48#
Feb  1 10:52 #traj_comp.xtc.47#
Feb  1 10:52 #traj_comp.xtc.46#
Feb  1 10:52 #traj_comp.xtc.45#
Feb  1 10:52 #traj_comp.xtc.44#
Feb  1 10:52 #traj_comp.xtc.43#
Feb  1 10:52 #traj_comp.xtc.42#
Feb  1 10:52 #traj_comp.xtc.41#
Feb  1 10:52 #traj_comp.xtc.40#
Feb  1 10:52 #traj_comp.xtc.39#
Feb  1 10:52 traj_comp.xtc
Feb  1 10:52 #md.log.70#
Feb  1 10:52 #md.log.69#
Feb  1 10:52 #md.log.68#
Feb  1 10:52 #md.log.67#
Feb  1 10:52 #md.log.66#
Feb  1 10:52 #md.log.65#
Feb  1 10:52 #md.log.64#
Feb  1 10:52 #md.log.63#
Feb  1 10:52 #md.log.62#
Feb  1 10:52 #md.log.61#
Feb  1 10:52 #md.log.60#
Feb  1 10:52 #md.log.59#
Feb  1 10:52 #md.log.58#
Feb  1 10:52 #md.log.57#
Feb  1 10:52 #md.log.56#
Feb  1 10:52 #md.log.55#
Feb  1 10:52 #md.log.54#
Feb  1 10:52 md.log
Feb  1 10:52 6ter.log

*KINDLY GET LOG FROM ATTACHMENT*
​
 6ter.log

​
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[gmx-users] Simulated annealing

[Venkat Raman]

Hi all,
   I am using Gromacs version 4.5.6 for peptide simulation. The
structure of the peptide (16mer) was predicted from Pepfold3 server. I did
Simulated annealing so that the side chains get properly oriented and the
predicted structure will reach its global optimum so that the structure
becomes more stable for production run. I have doubt in the mdp paramteres
regarding position restraints and the annealing time and temperature. I
tried with position restraints so that the backbone is restrained and the
side chains are free to move. The annealing was pretty good. I did SA after
NVT. I dont know to proceed further. How to finalize the mdp parameters
like pressure couping and generate velocities for simulated annealing?

Thanks in advance.
K.L. Venkatraman
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Re: [gmx-users] How to solvate particular regions in simulation box

[Venkat Reddy]

Hi Tsjerk,
Thank you for the quick reply. I will use "insane" tool to solvate the
capsid. But my capsid has around 2 million atoms and the box dimension is
approx. 500 x 500 x 500 A3. Can "insane" handle such a huge system?

With regards
Venkat

On Wed, Jul 13, 2016 at 12:35 PM, Tsjerk Wassenaar <tsje...@gmail.com>
wrote:

> Hi Venkat,
>
> First, note that there are no such things as hollow ('vacuum-filled' :p)
> proteins in nature. Simulating a capsid without contents is probably
> non-sensical.
> Besides that, you could try insane (http://cgmartini.nl/index.php/insane).
> By default it excludes the inside of a protein for placement of solvent.
>
> Cheers,
>
> Tsjerk
>
> On Wed, Jul 13, 2016 at 6:50 AM, Venkat Reddy <venkat...@gmail.com> wrote:
>
> > Dear all,
> > I am trying to simulate virus hollow capsid using gromos54a7 forcefield.
> > Since the capsid is hollow, I don't want water inside the capsid. But the
> > "gmx solvate" command solvates the hollow region of capsid also. So,
> every
> > time I manually remove the water  located inside the capsid as follows.
> >
> > 1) I find the com of protein using gmx traj -f -s -com -ox
> > 2) Using VMD, I extract out all the water molecules with in 'r' of
> capsid.
> > 3) I proceed to energy minimization, equillibration, and final dynamics.
> >
> > But the above mentioned process is not always fruitful, particularly when
> > the system is very big. Hence, I would like to know whether is there any
> > trick to solvate only certain regions (solvate only the regions which are
> > at 'r' distance from the com of protein) in the simulation box?
> >
> > Thanks and regards
> >
> > With best wishes
> > Venkat Reddy Chirasani
> > PhD student
> > Laboratory of Computational Biophysics
> > Department of Biotechnology
> > IIT Madras
> > Chennai
> > INDIA-600036
> > --
> > Gromacs Users mailing list
> >
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>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
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>



-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036
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Re: [gmx-users] How to initiate parallel run on GPU cluster

[Venkat Reddy]

Thank you Mark for the suggestion. I will convey the message to our system
admin. to solve the issue. thanks again for the valuable inputs.

On Thu, Apr 7, 2016 at 7:02 PM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> As you can see in that log file, you are only getting a single rank, so
> that's all that GROMACS can use. You need to troubleshoot your use of PBS
> and mpiexec so that you get four ranks placed two on each node. We can't
> read your cluster's docs or talk to your sysadmins :-)
>
> (And while you're at it, get them to compile with something less
> prehistoric than gcc 4.4. For many runs, you're likely to be bound by CPU
> performance with two K40s per node, and more recent compilers will be
> better...)
>
> Mark
>
> On Thu, Apr 7, 2016 at 3:16 PM Venkat Reddy <venkat...@gmail.com> wrote:
>
> > Dear Szilárd Páll,
> > Thanks for the response.
> >
> > My PBS script to launch the run is:
> >
> > #! /bin/bash
> > #PBS -l cput=5000:00:00
> > #PBS -l select=2:ncpus=16:ngpus=2
> > #PBS -e errorfile.err
> > #PBS -o logfile.log
> > tpdir=`echo $PBS_JOBID | cut -f 1 -d .`
> > tempdir=$HOME/work/job$tpdir
> > mkdir -p $tempdir
> > cd $tempdir
> > cp -R $PBS_O_WORKDIR/* .
> > mpiexec.hydra -np 4 -hostfile $PBS_NODEFILE /Apps/gromacs512/bin/gmx_mpi
> > mdrun -v -dlb yes  -ntomp 16 -s equilibration3.tpr
> >
> > Interestingly, I am using the same script to run CPU only jobs, which are
> > not creating any problems.
> >
> > Please check the generated log file here:
> > https://www.dropbox.com/s/dtfsuh6dv635n6q/md.log?dl=0
> >
> >
> >
> >
> > On Thu, Apr 7, 2016 at 6:18 PM, Szilárd Páll <pall.szil...@gmail.com>
> > wrote:
> >
> > > On Thu, Apr 7, 2016 at 2:35 PM, Venkat Reddy <venkat...@gmail.com>
> > wrote:
> > > > Thank you Mark for the quick response.
> > > > I tried to change -np option to 4. But it seems that mdrun is using
> > only
> > > > one GPU in single node with four ranks. The nvidia-smi command shows
> > > >
> > > > |0  7977C   /Apps/gromacs512/bin/gmx_mpi
> > > > 130MiB |
> > > > |0  7978C   /Apps/gromacs512/bin/gmx_mpi
> > > > 130MiB |
> > > > |0  7979C   /Apps/gromacs512/bin/gmx_mpi
> > > > 130MiB |
> > > > |0  7980C   /Apps/gromacs512/bin/gmx_mpi
> > > > 130MiB |
> > >
> > > No command line, no log file shown nothing to comment on.
> > >
> > > Additionally, if all four ranks you requested are on the same node
> > > rather than split over two nodes, that likely means you're using an
> > > incorrect job script -- definitely not a GROMACS issue. Please make
> > > sure you can launch an MPI "Hello world" program over multiple nodes
> > > first.
> > >
> > >
> > > > Also the job folder has four backed up copies of same run.
> > > >
> > > > On Thu, Apr 7, 2016 at 5:07 PM, Mark Abraham <
> mark.j.abra...@gmail.com
> > >
> > > > wrote:
> > > >
> > > >> Hi,
> > > >>
> > > >> mpiexec.hydra -np 1 asks for a single MPI rank, which is what you
> got.
> > > But
> > > >> you need at least two, ie. at least one on each rank, and at least
> > four
> > > if
> > > >> you want to make use of the two GPUs on each of two nodes.
> > > >>
> > > >> Mark
> > > >>
> > > >>
> > > >> On Thu, Apr 7, 2016 at 1:14 PM Venkat Reddy <venkat...@gmail.com>
> > > wrote:
> > > >>
> > > >> > Dear all,
> > > >> >
> > > >> > Please neglect my previous mail which was incomplete.
> > > >> >
> > > >> > I am trying to execute mdrun our GPU cluster with 7 nodes where
> each
> > > node
> > > >> > is populated by 16 processors and two K40 GPU cards. I have no
> > problem
> > > >> with
> > > >> > mdrun on single node. However, when I try to execute parallel run
> on
> > > two
> > > >> > nodes with gmx_mpi executable (gromacs-5.1.2),  the performance is
> > > very
> > > >> > slow. When I logged into individual nodes, I found that mdrun is
> not
> > > >> > utilizing both GPUs. The generated log file shows the following
> > > message.
> > > >>

Re: [gmx-users] How to initiate parallel run on GPU cluster

[Venkat Reddy]

Dear Szilárd Páll,
Thanks for the response.

My PBS script to launch the run is:

#! /bin/bash
#PBS -l cput=5000:00:00
#PBS -l select=2:ncpus=16:ngpus=2
#PBS -e errorfile.err
#PBS -o logfile.log
tpdir=`echo $PBS_JOBID | cut -f 1 -d .`
tempdir=$HOME/work/job$tpdir
mkdir -p $tempdir
cd $tempdir
cp -R $PBS_O_WORKDIR/* .
mpiexec.hydra -np 4 -hostfile $PBS_NODEFILE /Apps/gromacs512/bin/gmx_mpi
mdrun -v -dlb yes  -ntomp 16 -s equilibration3.tpr

Interestingly, I am using the same script to run CPU only jobs, which are
not creating any problems.

Please check the generated log file here:
https://www.dropbox.com/s/dtfsuh6dv635n6q/md.log?dl=0




On Thu, Apr 7, 2016 at 6:18 PM, Szilárd Páll <pall.szil...@gmail.com> wrote:

> On Thu, Apr 7, 2016 at 2:35 PM, Venkat Reddy <venkat...@gmail.com> wrote:
> > Thank you Mark for the quick response.
> > I tried to change -np option to 4. But it seems that mdrun is using only
> > one GPU in single node with four ranks. The nvidia-smi command shows
> >
> > |0  7977C   /Apps/gromacs512/bin/gmx_mpi
> > 130MiB |
> > |0  7978C   /Apps/gromacs512/bin/gmx_mpi
> > 130MiB |
> > |0  7979C   /Apps/gromacs512/bin/gmx_mpi
> > 130MiB |
> > |0  7980C   /Apps/gromacs512/bin/gmx_mpi
> > 130MiB |
>
> No command line, no log file shown nothing to comment on.
>
> Additionally, if all four ranks you requested are on the same node
> rather than split over two nodes, that likely means you're using an
> incorrect job script -- definitely not a GROMACS issue. Please make
> sure you can launch an MPI "Hello world" program over multiple nodes
> first.
>
>
> > Also the job folder has four backed up copies of same run.
> >
> > On Thu, Apr 7, 2016 at 5:07 PM, Mark Abraham <mark.j.abra...@gmail.com>
> > wrote:
> >
> >> Hi,
> >>
> >> mpiexec.hydra -np 1 asks for a single MPI rank, which is what you got.
> But
> >> you need at least two, ie. at least one on each rank, and at least four
> if
> >> you want to make use of the two GPUs on each of two nodes.
> >>
> >> Mark
> >>
> >>
> >> On Thu, Apr 7, 2016 at 1:14 PM Venkat Reddy <venkat...@gmail.com>
> wrote:
> >>
> >> > Dear all,
> >> >
> >> > Please neglect my previous mail which was incomplete.
> >> >
> >> > I am trying to execute mdrun our GPU cluster with 7 nodes where each
> node
> >> > is populated by 16 processors and two K40 GPU cards. I have no problem
> >> with
> >> > mdrun on single node. However, when I try to execute parallel run on
> two
> >> > nodes with gmx_mpi executable (gromacs-5.1.2),  the performance is
> very
> >> > slow. When I logged into individual nodes, I found that mdrun is not
> >> > utilizing both GPUs. The generated log file shows the following
> message.
> >> >
> >> > Using 1 MPI process
> >> > Using 16 OpenMP threads
> >> >
> >> > 2 compatible GPUs are present, with IDs 0,1
> >> > 1 GPU auto-selected for this run.
> >> > Mapping of GPU ID to the 1 PP rank in this node: 0
> >> >
> >> >
> >> > NOTE: potentially sub-optimal launch configuration, gmx_mpi started
> with
> >> > less
> >> >   PP MPI process per node than GPUs available.
> >> >   Each PP MPI process can use only one GPU, 1 GPU per node will be
> >> > used.
> >> >
> >> > I read the manual and instructions in
> >> >
> >> >
> >>
> http://manual.gromacs.org/documentation/5.1/user-guide/mdrun-performance.html
> >> > to
> >> > execute the parallel run. But I couldn't find the right flags to
> initiate
> >> > it. Please help me in this aspect. The script I used to execute the
> >> > parallel run is given below.
> >> >
> >> > #! /bin/bash
> >> > #PBS -l cput=5000:00:00
> >> > #PBS -l select=2:ncpus=16:ngpus=2
> >> > #PBS -e errorfile.err
> >> > #PBS -o logfile.log
> >> > tpdir=`echo $PBS_JOBID | cut -f 1 -d .`
> >> > tempdir=$HOME/work/job$tpdir
> >> > mkdir -p $tempdir
> >> > cd $tempdir
> >> > cp -R $PBS_O_WORKDIR/* .
> >> > mpiexec.hydra -np 1 -hostfile $PBS_NODEFILE
> /Apps/gromacs512/bin/gmx_mpi
> >> > mdrun -v -dlb yes  -ntomp 16 -s equilibration3.tpr
> >> >
> >> >
> >> >
> >> > --
> >> > With Best Wishes
>

Re: [gmx-users] How to initiate parallel run on GPU cluster

[Venkat Reddy]

Thank you Mark for the quick response.
I tried to change -np option to 4. But it seems that mdrun is using only
one GPU in single node with four ranks. The nvidia-smi command shows

|0  7977C   /Apps/gromacs512/bin/gmx_mpi
130MiB |
|0  7978C   /Apps/gromacs512/bin/gmx_mpi
130MiB |
|0  7979C   /Apps/gromacs512/bin/gmx_mpi
130MiB |
|0  7980C   /Apps/gromacs512/bin/gmx_mpi
130MiB |

Also the job folder has four backed up copies of same run.

On Thu, Apr 7, 2016 at 5:07 PM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> mpiexec.hydra -np 1 asks for a single MPI rank, which is what you got. But
> you need at least two, ie. at least one on each rank, and at least four if
> you want to make use of the two GPUs on each of two nodes.
>
> Mark
>
>
> On Thu, Apr 7, 2016 at 1:14 PM Venkat Reddy <venkat...@gmail.com> wrote:
>
> > Dear all,
> >
> > Please neglect my previous mail which was incomplete.
> >
> > I am trying to execute mdrun our GPU cluster with 7 nodes where each node
> > is populated by 16 processors and two K40 GPU cards. I have no problem
> with
> > mdrun on single node. However, when I try to execute parallel run on two
> > nodes with gmx_mpi executable (gromacs-5.1.2),  the performance is very
> > slow. When I logged into individual nodes, I found that mdrun is not
> > utilizing both GPUs. The generated log file shows the following message.
> >
> > Using 1 MPI process
> > Using 16 OpenMP threads
> >
> > 2 compatible GPUs are present, with IDs 0,1
> > 1 GPU auto-selected for this run.
> > Mapping of GPU ID to the 1 PP rank in this node: 0
> >
> >
> > NOTE: potentially sub-optimal launch configuration, gmx_mpi started with
> > less
> >   PP MPI process per node than GPUs available.
> >   Each PP MPI process can use only one GPU, 1 GPU per node will be
> > used.
> >
> > I read the manual and instructions in
> >
> >
> http://manual.gromacs.org/documentation/5.1/user-guide/mdrun-performance.html
> > to
> > execute the parallel run. But I couldn't find the right flags to initiate
> > it. Please help me in this aspect. The script I used to execute the
> > parallel run is given below.
> >
> > #! /bin/bash
> > #PBS -l cput=5000:00:00
> > #PBS -l select=2:ncpus=16:ngpus=2
> > #PBS -e errorfile.err
> > #PBS -o logfile.log
> > tpdir=`echo $PBS_JOBID | cut -f 1 -d .`
> > tempdir=$HOME/work/job$tpdir
> > mkdir -p $tempdir
> > cd $tempdir
> > cp -R $PBS_O_WORKDIR/* .
> > mpiexec.hydra -np 1 -hostfile $PBS_NODEFILE /Apps/gromacs512/bin/gmx_mpi
> > mdrun -v -dlb yes  -ntomp 16 -s equilibration3.tpr
> >
> >
> >
> > --
> > 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
> >
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> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
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-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036
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[gmx-users] How to initiate parallel run on GPU cluster

[Venkat Reddy]

Dear all,
I am trying to execute mdrun our GPU
#! /bin/bash
#PBS -l cput=5000:00:00
#PBS -l select=2:ncpus=16:ngpus=2
#PBS -e errorfile.err
#PBS -o logfile.log
tpdir=`echo $PBS_JOBID | cut -f 1 -d .`
tempdir=$HOME/work/job$tpdir
mkdir -p $tempdir
cd $tempdir
cp -R $PBS_O_WORKDIR/* .
mpiexec.hydra -np 2 -hostfile $PBS_NODEFILE /Apps/gromacs512/bin/gmx_mpi
mdrun -v -dlb yes  -ntomp 16 -gpu_id 0101 -s equilibration3.tpr

Fatal error:
Incorrect launch configuration: mismatching number of PP MPI processes and
GPUs per node. gmx_mpi was started with 1 PP MPI process per node, but you
provided 4 GPUs.

-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036
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Re: [gmx-users] velocity in trjconv

[Venkat Reddy]

Hi,
Probably you should use '-novel'

On Mon, Oct 12, 2015 at 10:23 PM, Parvez Mh <parvezm...@gmail.com> wrote:

> Dear all,
> I need to convert .trr file into .gro file without velocity. That's why i
> used '-vel no' , but i got error 'invalid argument no'. Can any tell me how
> to use -vel option for not writing velocity in .gro file .
>
> Regards
> Masrul
> --
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-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036
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Re: [gmx-users] Analysis of old xtc file using gromacs-5 tools

[Venkat Reddy]

Hi,
I can check all the possible combinations you listed in
http://redmine.gromacs.org/issues/1834. Since my programming capability is
limited, please direct me how to proceed for solving this issue?

On Tue, Oct 6, 2015 at 9:00 PM, Teemu Murtola <teemu.murt...@gmail.com>
wrote:

> Thanks for the clarification. I updated the Redmine issue (
> http://redmine.gromacs.org/issues/1834) with a summary and next steps. I
> unfortunately do not have access to various systems to test the issue, but
> I put some guesses on the possible reasons in the issue.
>
> Best regards,
> Teemu
>
> On Tue, Oct 6, 2015, 07:37 Venkat Reddy <venkat...@gmail.com> wrote:
>
> > Hi,
> > Sorry for the confusion. Now I have generated a small xtc file and a very
> > big pdb file. I can able to access small xtc file but unable to read the
> > large pdb file (~10GB) (terminating with the same error as reported
> > earlier). Does it mean my installation has some problem?
> >
> > On Mon, Oct 5, 2015 at 7:41 PM, Teemu Murtola <teemu.murt...@gmail.com>
> > wrote:
> >
> > > Hi,
> > >
> > > That unfortunately doesn't tell us anything, since 1.5GB can still be
> > read
> > > with 32-bit file operations. You didn't answer any of the questions:
> can
> > > you open very small xtc files, or very large (requiring 64-bit access)
> > > gro/pdb files, or not? We are still thinking that you should be able to
> > > open any files smaller than 2GB just fine, but you are making confusing
> > > claims that seem to contradict this, so this needs to be sorted out
> > before
> > > we can really conclude anything.
> > >
> > > Best regards,
> > > Teemu
> > >
> > > On Mon, Oct 5, 2015, 08:32 Venkat Reddy <venkat...@gmail.com> wrote:
> > >
> > > > Hi,
> > > > Sorry for the delay in reply.
> > > > I am able to access pdb/gro files of size 1.5 GB with Gromacs-5.1
> > > version.
> > > > My Desktop is 32-bit whereas my xtc files were generated on our super
> > > > cluster, which runs on 64-bit O.S.
> > > >
> > > > On Fri, Oct 2, 2015 at 9:46 AM, Teemu Murtola <
> teemu.murt...@gmail.com
> > >
> > > > wrote:
> > > >
> > > > > Hi,
> > > > >
> > > > > On Thu, Oct 1, 2015 at 6:30 PM Szilárd Páll <
> pall.szil...@gmail.com>
> > > > > wrote:
> > > > >
> > > > > > On Thu, Oct 1, 2015 at 8:01 AM, Venkat Reddy <
> venkat...@gmail.com>
> > > > > wrote:
> > > > > > > Gromacs-5.1 version can not read xtc files. However, it can
> > access
> > > > > single
> > > > > > > frame gro/pdb files.
> > > > > > >
> > > > > >
> > > > > > That's a bold claim that IMO requires equally strong proof.
> > > > > >
> > > > >
> > > > > I agree with Szilard. Are you saying that you cannot even read a
> > > > > single-frame xtc file with just a few kB in size? How about other
> > > binary
> > > > > files (e.g., trr)? How about large (>2GB) gro files?
> > > > >
> > > > > In your other mail to the list you were talking about a 32-bit
> Ubuntu
> > > VM.
> > > > > > Are you sure you're not running into in incompatibility issue
> > between
> > > > the
> > > > > > 32-bit binaries vs 64-bit xtc file(s) you're trying to read?
> > > > > >
> > > > >
> > > > > I would still suspect that the underlying reason is that for some
> > > reason,
> > > > > 5.1 gets compiled without large file support in your system, which
> > > makes
> > > > > even plain fopen() fail on large files. The build system should
> give
> > an
> > > > > error if it cannot find 64-bit file support, but the check may be
> > > > > imperfect. Someone who can reproduce the issue (i.e., has access
> to a
> > > > > similar OS and other environment) should try what is actually
> > required
> > > to
> > > > > get 64-bit file support working there. Based on the information you
> > > > posted
> > > > > in Redmine, the build system already checks that off_t is 64-bit
> > > without
> > > > > any extra defines on your system. The checks in the build system
> have
> > > not
> > > > > change

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

[Venkat Reddy]

Hi,
Sorry for the confusion. Now I have generated a small xtc file and a very
big pdb file. I can able to access small xtc file but unable to read the
large pdb file (~10GB) (terminating with the same error as reported
earlier). Does it mean my installation has some problem?

On Mon, Oct 5, 2015 at 7:41 PM, Teemu Murtola <teemu.murt...@gmail.com>
wrote:

> Hi,
>
> That unfortunately doesn't tell us anything, since 1.5GB can still be read
> with 32-bit file operations. You didn't answer any of the questions: can
> you open very small xtc files, or very large (requiring 64-bit access)
> gro/pdb files, or not? We are still thinking that you should be able to
> open any files smaller than 2GB just fine, but you are making confusing
> claims that seem to contradict this, so this needs to be sorted out before
> we can really conclude anything.
>
> Best regards,
> Teemu
>
> On Mon, Oct 5, 2015, 08:32 Venkat Reddy <venkat...@gmail.com> wrote:
>
> > Hi,
> > Sorry for the delay in reply.
> > I am able to access pdb/gro files of size 1.5 GB with Gromacs-5.1
> version.
> > My Desktop is 32-bit whereas my xtc files were generated on our super
> > cluster, which runs on 64-bit O.S.
> >
> > On Fri, Oct 2, 2015 at 9:46 AM, Teemu Murtola <teemu.murt...@gmail.com>
> > wrote:
> >
> > > Hi,
> > >
> > > On Thu, Oct 1, 2015 at 6:30 PM Szilárd Páll <pall.szil...@gmail.com>
> > > wrote:
> > >
> > > > On Thu, Oct 1, 2015 at 8:01 AM, Venkat Reddy <venkat...@gmail.com>
> > > wrote:
> > > > > Gromacs-5.1 version can not read xtc files. However, it can access
> > > single
> > > > > frame gro/pdb files.
> > > > >
> > > >
> > > > That's a bold claim that IMO requires equally strong proof.
> > > >
> > >
> > > I agree with Szilard. Are you saying that you cannot even read a
> > > single-frame xtc file with just a few kB in size? How about other
> binary
> > > files (e.g., trr)? How about large (>2GB) gro files?
> > >
> > > In your other mail to the list you were talking about a 32-bit Ubuntu
> VM.
> > > > Are you sure you're not running into in incompatibility issue between
> > the
> > > > 32-bit binaries vs 64-bit xtc file(s) you're trying to read?
> > > >
> > >
> > > I would still suspect that the underlying reason is that for some
> reason,
> > > 5.1 gets compiled without large file support in your system, which
> makes
> > > even plain fopen() fail on large files. The build system should give an
> > > error if it cannot find 64-bit file support, but the check may be
> > > imperfect. Someone who can reproduce the issue (i.e., has access to a
> > > similar OS and other environment) should try what is actually required
> to
> > > get 64-bit file support working there. Based on the information you
> > posted
> > > in Redmine, the build system already checks that off_t is 64-bit
> without
> > > any extra defines on your system. The checks in the build system have
> not
> > > changed between 5.0 and 5.1, though.
> > >
> > > Teemu
> > > --
> > > 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!
> >
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> >
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> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
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>



-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036
-- 
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Re: [gmx-users] Analysis of old xtc file using gromacs-5 tools

[Venkat Reddy]

Hi,
Sorry for the delay in reply.
I am able to access pdb/gro files of size 1.5 GB with Gromacs-5.1 version.
My Desktop is 32-bit whereas my xtc files were generated on our super
cluster, which runs on 64-bit O.S.

On Fri, Oct 2, 2015 at 9:46 AM, Teemu Murtola <teemu.murt...@gmail.com>
wrote:

> Hi,
>
> On Thu, Oct 1, 2015 at 6:30 PM Szilárd Páll <pall.szil...@gmail.com>
> wrote:
>
> > On Thu, Oct 1, 2015 at 8:01 AM, Venkat Reddy <venkat...@gmail.com>
> wrote:
> > > Gromacs-5.1 version can not read xtc files. However, it can access
> single
> > > frame gro/pdb files.
> > >
> >
> > That's a bold claim that IMO requires equally strong proof.
> >
>
> I agree with Szilard. Are you saying that you cannot even read a
> single-frame xtc file with just a few kB in size? How about other binary
> files (e.g., trr)? How about large (>2GB) gro files?
>
> In your other mail to the list you were talking about a 32-bit Ubuntu VM.
> > Are you sure you're not running into in incompatibility issue between the
> > 32-bit binaries vs 64-bit xtc file(s) you're trying to read?
> >
>
> I would still suspect that the underlying reason is that for some reason,
> 5.1 gets compiled without large file support in your system, which makes
> even plain fopen() fail on large files. The build system should give an
> error if it cannot find 64-bit file support, but the check may be
> imperfect. Someone who can reproduce the issue (i.e., has access to a
> similar OS and other environment) should try what is actually required to
> get 64-bit file support working there. Based on the information you posted
> in Redmine, the build system already checks that off_t is 64-bit without
> any extra defines on your system. The checks in the build system have not
> changed between 5.0 and 5.1, though.
>
> Teemu
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
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>



-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036
-- 
Gromacs Users mailing list

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

[Venkat Reddy]

Hi
Gromacs-5.1 version can not read xtc files. However, it can access single
frame gro/pdb files.


On Thu, Oct 1, 2015 at 10:44 AM, Teemu Murtola <teemu.murt...@gmail.com>
wrote:

> Are you saying that you cannot open any xtc files? If that is the case,
> then this may not have anything to do with 64-bit for support. Can your
> Gromacs compilation open any files? You will need to isolate the problem a
> bit to help diagnosing it, since we don't have access to your system.
>
> Teemu
>
> On Thu, Oct 1, 2015, 07:48 Venkat Reddy <venkat...@gmail.com> wrote:
>
> > Hi,
> > 1) Yes, I can access the same xtc with older gromacs versions.
> > 2) I can't access even smaller xtc files with 5.1
> > I will file a bug report for the same.
> > Thank you
> >
> >
> >
> > On Wed, Sep 30, 2015 at 9:28 PM, Teemu Murtola <teemu.murt...@gmail.com>
> > wrote:
> >
> > > Hi,
> > >
> > > This sounds like the build system is not compiling Gromacs with 64-bit
> > file
> > > support like it should. Can you access the same file on the same system
> > > with earlier Gromacs versions? Can you access smaller files with 5.1?
> > >
> > > Could you file a bug report at redmine.gromacs.org, and include at
> least
> > > the following:
> > > * information on your operating system
> > > * contents of CMakeCache.txt, src/config.h, and src/gmxpre-config.h
> from
> > > your build tree
> > > * how you invoked cmake to configure the build.
> > >
> > > Teemu
> > >
> > > On Wed, Sep 30, 2015, 11:59 Venkat Reddy <venkat...@gmail.com> wrote:
> > >
> > > > Hi Teemu,
> > > > Thanks for the prompt reply. Yes, the xtc file size is larger than
> 2GB
> > > > (approx. 50GB) and both system.xtc and traj.xtc are same files. I am
> > > > extremely sorry for the confusion :)
> > > >
> > > > On Wed, Sep 30, 2015 at 11:31 AM, Teemu Murtola <
> > teemu.murt...@gmail.com
> > > >
> > > > wrote:
> > > >
> > > > > Thanks for testing it, I see that there is still room for
> improvement
> > > in
> > > > > getting more context information into the error messages. I'm a bit
> > > > > confused by the difference between your original report of
> system.xtc
> > > vs
> > > > > traj.xtc in the new message, but that may not matter that much. Is
> > your
> > > > xtc
> > > > > file larger that 2GB in size?
> > > > >
> > > > > On Wed, Sep 30, 2015, 07:53 Venkat Reddy <venkat...@gmail.com>
> > wrote:
> > > > >
> > > > > > 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 <
> > > > teemu.murt...@gmail.com>
> > > > > > wrote:
> > > > > >
> > > > > > > Hi,
> > > > > > >
> > > > > > > I now changed the check to provide more details (in 5140
> > > > > > > <https://gerrit.gromacs.org/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 

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

[Venkat Reddy]

Hi Teemu,
Thanks for the prompt reply. Yes, the xtc file size is larger than 2GB
(approx. 50GB) and both system.xtc and traj.xtc are same files. I am
extremely sorry for the confusion :)

On Wed, Sep 30, 2015 at 11:31 AM, Teemu Murtola <teemu.murt...@gmail.com>
wrote:

> Thanks for testing it, I see that there is still room for improvement in
> getting more context information into the error messages. I'm a bit
> confused by the difference between your original report of system.xtc vs
> traj.xtc in the new message, but that may not matter that much. Is your xtc
> file larger that 2GB in size?
>
> On Wed, Sep 30, 2015, 07:53 Venkat Reddy <venkat...@gmail.com> wrote:
>
> > 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 <teemu.murt...@gmail.com>
> > wrote:
> >
> > > Hi,
> > >
> > > I now changed the check to provide more details (in 5140
> > > <https://gerrit.gromacs.org/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 <
> teemu.murt...@gmail.com>
> > > 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 <venkat...@gmail.com>
> 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 <
> tsje...@gmail.com
> > >
> > > >> 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" <venkat...@gmail.com>
> 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 er

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

[Venkat Reddy]

Hi,
1) Yes, I can access the same xtc with older gromacs versions.
2) I can't access even smaller xtc files with 5.1
I will file a bug report for the same.
Thank you



On Wed, Sep 30, 2015 at 9:28 PM, Teemu Murtola <teemu.murt...@gmail.com>
wrote:

> Hi,
>
> This sounds like the build system is not compiling Gromacs with 64-bit file
> support like it should. Can you access the same file on the same system
> with earlier Gromacs versions? Can you access smaller files with 5.1?
>
> Could you file a bug report at redmine.gromacs.org, and include at least
> the following:
> * information on your operating system
> * contents of CMakeCache.txt, src/config.h, and src/gmxpre-config.h from
> your build tree
> * how you invoked cmake to configure the build.
>
> Teemu
>
> On Wed, Sep 30, 2015, 11:59 Venkat Reddy <venkat...@gmail.com> wrote:
>
> > Hi Teemu,
> > Thanks for the prompt reply. Yes, the xtc file size is larger than 2GB
> > (approx. 50GB) and both system.xtc and traj.xtc are same files. I am
> > extremely sorry for the confusion :)
> >
> > On Wed, Sep 30, 2015 at 11:31 AM, Teemu Murtola <teemu.murt...@gmail.com
> >
> > wrote:
> >
> > > Thanks for testing it, I see that there is still room for improvement
> in
> > > getting more context information into the error messages. I'm a bit
> > > confused by the difference between your original report of system.xtc
> vs
> > > traj.xtc in the new message, but that may not matter that much. Is your
> > xtc
> > > file larger that 2GB in size?
> > >
> > > On Wed, Sep 30, 2015, 07:53 Venkat Reddy <venkat...@gmail.com> wrote:
> > >
> > > > 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 <
> > teemu.murt...@gmail.com>
> > > > wrote:
> > > >
> > > > > Hi,
> > > > >
> > > > > I now changed the check to provide more details (in 5140
> > > > > <https://gerrit.gromacs.org/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 <
> > > teemu.murt...@gmail.com>
> > > > > 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
> furt

[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
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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 <teemu.murt...@gmail.com>
wrote:

> Hi,
>
> I now changed the check to provide more details (in 5140
> <https://gerrit.gromacs.org/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 <teemu.murt...@gmail.com>
> 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 <venkat...@gmail.com> 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 <tsje...@gmail.com>
> >> 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" <venkat...@gmail.com> 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/Maili

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

[Venkat Reddy]

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!

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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Regarding engineered residue topology

[Venkat Reddy]

Thank you Justin for clear explanation.
However, the parameters are available for
CX CT CT_2   HC  3  0.96650   2.89951   0.0  -3.86601
0.000   0.000;
C* CT CT_2   HC  3  0.96650   2.89951   0.0  -3.86601
0.000   0.000 ;
So, can I apply the same for CT-CT_2-CT-HC dihedral?

Thank you for your valuable time and concern.

On Mon, Jul 27, 2015 at 5:16 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 7/27/15 1:21 AM, Venkat Reddy wrote:

 Dear Justin,
 Thank you for the prompt reply. I have checked the topology file once
 again
 and confirmed the dihedral (CB2-CA-CB1-HB11) thats creating problem. The
 Aib parameters are indeed available for OPLS-AA ff. But I couldn't locate
 the dihedral parameters for the above mentioned dihedral angle in
 ffbonded.itp file. However I found dihedral parameters for X-CA-CB-X. So,
 can I use X-CA-CB-X parameters for CB2-CA-CB1-HB11 dihedral?


 You're confusing atom names and atom types.  The names are totally
 irrelevant for parameter assignment.  The CB2-C1-CB1-HB11 dihedral has a
 sequence of nonbonded types of opls_135-opls_225B-opls_135-opls_140, which
 have bonded types (see second column of ffnonbonded.itp) of CT-CT_2-CT-HC.
 So the parameters you need are for CT-CT_2-CT-HC, which are indeed not in
 ffbonded.itp.

 -Justin


  On Mon, Jul 27, 2015 at 5:46 AM, Justin Lemkul jalem...@vt.edu wrote:



 On 7/24/15 9:20 AM, Venkat Reddy wrote:

  Dear all,
 I am trying to simulate a peptide with engineered residues like Aib
 (alpha
 amino-isobutyric acid). I am trying to use OPLS-aa forcefield. Though
 everything went well initially during topology generation, grompp showed
 the following error.

 ERROR 1 [file topol.top, line 2316]:
 No default Ryckaert-Bell. types
 ERROR 2 [file topol.top, line 2317]:
 No default Ryckaert-Bell. types
 ERROR 3 [file topol.top, line 2318]:
 No default Ryckaert-Bell. types
 ERROR 4 [file topol.top, line 2325]:
 No default Ryckaert-Bell. types
 ERROR 5 [file topol.top, line 2326]:
 No default Ryckaert-Bell. types
 ERROR 6 [file topol.top, line 2327]:
 No default Ryckaert-Bell. types

 The cross-check with topolo.top identified the dihedral CB2-CA-CB1-HB11
 is
 throwing the error. My question is, even though the parameters for Aib
 are
 available in OPLS ff, why I am getting this error?


  grompp doesn't lie.  Either you're looking at the wrong lines or you're
 looking at the wrong parameters.  Some residues are constructed for
 convenience but if they're not official then there may be problems.

 -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.





 --
 ==

 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.




-- 
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!

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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Regarding engineered residue topology

[Venkat Reddy]

Thanks Justin. How shall I tackle this problem? Can I use any other AA
force field, say CHARMM27?
The Aib parameters are available in an old gromacs forcefield (mentioned as
DEPRECATED in gromacs-4.5.7), which hasn't showed any error while
simulating the same system.

On Tue, Jul 28, 2015 at 6:07 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 7/28/15 3:30 AM, Venkat Reddy wrote:

 Thank you Justin for clear explanation.
 However, the parameters are available for
 CX CT CT_2   HC  3  0.96650   2.89951   0.0  -3.86601
 0.000   0.000;
 C* CT CT_2   HC  3  0.96650   2.89951   0.0  -3.86601
 0.000   0.000 ;
 So, can I apply the same for CT-CT_2-CT-HC dihedral?


 No idea.  Generally dihedrals are the least transferable of any bonded
 parameter, so there's no reason to assume that you can apply the parameters
 from other interactions to any other given interaction.

 -Justin


  Thank you for your valuable time and concern.

 On Mon, Jul 27, 2015 at 5:16 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 7/27/15 1:21 AM, Venkat Reddy wrote:

  Dear Justin,
 Thank you for the prompt reply. I have checked the topology file once
 again
 and confirmed the dihedral (CB2-CA-CB1-HB11) thats creating problem. The
 Aib parameters are indeed available for OPLS-AA ff. But I couldn't
 locate
 the dihedral parameters for the above mentioned dihedral angle in
 ffbonded.itp file. However I found dihedral parameters for X-CA-CB-X.
 So,
 can I use X-CA-CB-X parameters for CB2-CA-CB1-HB11 dihedral?


  You're confusing atom names and atom types.  The names are totally
 irrelevant for parameter assignment.  The CB2-C1-CB1-HB11 dihedral has a
 sequence of nonbonded types of opls_135-opls_225B-opls_135-opls_140,
 which
 have bonded types (see second column of ffnonbonded.itp) of
 CT-CT_2-CT-HC.
 So the parameters you need are for CT-CT_2-CT-HC, which are indeed not in
 ffbonded.itp.

 -Justin


   On Mon, Jul 27, 2015 at 5:46 AM, Justin Lemkul jalem...@vt.edu
 wrote:




 On 7/24/15 9:20 AM, Venkat Reddy wrote:

   Dear all,

 I am trying to simulate a peptide with engineered residues like Aib
 (alpha
 amino-isobutyric acid). I am trying to use OPLS-aa forcefield. Though
 everything went well initially during topology generation, grompp
 showed
 the following error.

 ERROR 1 [file topol.top, line 2316]:
  No default Ryckaert-Bell. types
 ERROR 2 [file topol.top, line 2317]:
  No default Ryckaert-Bell. types
 ERROR 3 [file topol.top, line 2318]:
  No default Ryckaert-Bell. types
 ERROR 4 [file topol.top, line 2325]:
  No default Ryckaert-Bell. types
 ERROR 5 [file topol.top, line 2326]:
  No default Ryckaert-Bell. types
 ERROR 6 [file topol.top, line 2327]:
  No default Ryckaert-Bell. types

 The cross-check with topolo.top identified the dihedral
 CB2-CA-CB1-HB11
 is
 throwing the error. My question is, even though the parameters for Aib
 are
 available in OPLS ff, why I am getting this error?


   grompp doesn't lie.  Either you're looking at the wrong lines or
 you're

 looking at the wrong parameters.  Some residues are constructed for
 convenience but if they're not official then there may be problems.

 -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!

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  --
 ==

 Justin A. Lemkul, Ph.D.
 Ruth L. Kirschstein NRSA Postdoctoral Fellow

 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 629
 University of Maryland, Baltimore
 20 Penn St.
 Baltimore, MD 21201

 jalem...@outerbanks.umaryland.edu | (410) 706-7441
 http://mackerell.umaryland.edu/~jalemkul

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 --
 ==

 Justin A. Lemkul, Ph.D.
 Ruth L. Kirschstein NRSA Postdoctoral Fellow

 Department of Pharmaceutical

Re: [gmx-users] Regarding engineered residue topology

[Venkat Reddy]

Dear Justin,
Thank you for the prompt reply. I have checked the topology file once again
and confirmed the dihedral (CB2-CA-CB1-HB11) thats creating problem. The
Aib parameters are indeed available for OPLS-AA ff. But I couldn't locate
the dihedral parameters for the above mentioned dihedral angle in
ffbonded.itp file. However I found dihedral parameters for X-CA-CB-X. So,
can I use X-CA-CB-X parameters for CB2-CA-CB1-HB11 dihedral?

On Mon, Jul 27, 2015 at 5:46 AM, Justin Lemkul jalem...@vt.edu wrote:



 On 7/24/15 9:20 AM, Venkat Reddy wrote:

 Dear all,
 I am trying to simulate a peptide with engineered residues like Aib (alpha
 amino-isobutyric acid). I am trying to use OPLS-aa forcefield. Though
 everything went well initially during topology generation, grompp showed
 the following error.

 ERROR 1 [file topol.top, line 2316]:
No default Ryckaert-Bell. types
 ERROR 2 [file topol.top, line 2317]:
No default Ryckaert-Bell. types
 ERROR 3 [file topol.top, line 2318]:
No default Ryckaert-Bell. types
 ERROR 4 [file topol.top, line 2325]:
No default Ryckaert-Bell. types
 ERROR 5 [file topol.top, line 2326]:
No default Ryckaert-Bell. types
 ERROR 6 [file topol.top, line 2327]:
No default Ryckaert-Bell. types

 The cross-check with topolo.top identified the dihedral CB2-CA-CB1-HB11 is
 throwing the error. My question is, even though the parameters for Aib are
 available in OPLS ff, why I am getting this error?


 grompp doesn't lie.  Either you're looking at the wrong lines or you're
 looking at the wrong parameters.  Some residues are constructed for
 convenience but if they're not official then there may be problems.

 -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
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-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036
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[gmx-users] Regarding engineered residue topology

[Venkat Reddy]

Dear all,
I am trying to simulate a peptide with engineered residues like Aib (alpha
amino-isobutyric acid). I am trying to use OPLS-aa forcefield. Though
everything went well initially during topology generation, grompp showed
the following error.

ERROR 1 [file topol.top, line 2316]:
  No default Ryckaert-Bell. types
ERROR 2 [file topol.top, line 2317]:
  No default Ryckaert-Bell. types
ERROR 3 [file topol.top, line 2318]:
  No default Ryckaert-Bell. types
ERROR 4 [file topol.top, line 2325]:
  No default Ryckaert-Bell. types
ERROR 5 [file topol.top, line 2326]:
  No default Ryckaert-Bell. types
ERROR 6 [file topol.top, line 2327]:
  No default Ryckaert-Bell. types

The cross-check with topolo.top identified the dihedral CB2-CA-CB1-HB11 is
throwing the error. My question is, even though the parameters for Aib are
available in OPLS ff, why I am getting this error?

Please help me in this regard

With regards
Venkat
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[gmx-users] RDF does not reach 1 for bulk

[Venkat Reddy]

Dear Gromacs users,

I would like to know why the normalized RDF data from g_rdf does not reach
1 for bulk?

As an alternative I tried using the raw data (i.e., by using the 'nonorm'
flag) and normalized the values by dividing them by  'rho*volume of bin',
which I believe is the standard method for normalization. Still I get the
trend obtained from the normalized data, where the end of the RDF curve
tapers downward, much below 1.

Kindly suggest how I could deal with this issue.

Thanks

-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036
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Re: [gmx-users] Charmm to gromacs conversion for lipids

[Venkat Reddy]

Thank you Justin for the great help you have done, as you always been. I
will download the latest updated CHARMM36 files.

On Fri, Nov 7, 2014 at 6:10 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 11/7/14 12:30 AM, Venkat Reddy wrote:

 Dear Justin,
 Please check the atom section of toppar_all36_lipid_cholesterol.str
 file
 that I pasted below.

 * Toppar stream file for cholesterol.  Stream following reading of
 * top_all36_lipid.rtf  and par_all36_lipid.rtf

 !reference
 !Suits, F., Pitman, M., MacKerell, A.D., Jr., Feller, S.E. Molecular
 Level
 !Organization of Saturated and Polyunsaturated Fatty Acids in a
 !Phosphatidylcholine Bilayer Containing Cholesterol Submitted
 !for publication


 I see where the problem is.  Note that this file says Submitted for
 publication, but it was actually published 10 years ago.  This stream file
 is outdated.  The CHL1 model I included in the CHARMM36 distribution is the
 current one, which uses CRL1 for C3 and a series of NBFIXes described in
 the 2012 paper by Lim et al. (full reference in forcefield.doc).

 You can get the latest, updated CHARMM36 force field files from
 http://mackerell.umaryland.edu/charmm_ff.shtml#charmm

 -Justin


  read rtf card append
 * cholesterol residues
 *

 RESI CHL1  0.00  !cholesterol (name to avoid conflict with
 choline)
 ! atoms names correspond to the correct cholesterol nomenclature
 GROUP
 ATOM C3   CTL1 0.14
 ATOM O3   OHL -0.66
 ATOM H3'  HOL  0.43
 ATOM H3   HAL1 0.09
 GROUP
 ATOM C4   CTL2-0.18
 ATOM H4A  HAL2 0.09
 ATOM H4B  HAL2 0.09
 GROUP
 ATOM C5   CEL1 0.00
 ATOM C6   CEL1-0.15
 ATOM H6   HEL1 0.15
 GROUP
 ATOM C7   CTL2-0.18
 ATOM H7A  HAL2 0.09
 ATOM H7B  HAL2 0.09
 GROUP
 ATOM C8   CTL1-0.09
 ATOM H8   HAL1 0.09
 GROUP
 ATOM C14  CTL1-0.09
 ATOM H14  HAL1 0.09
 GROUP
 ATOM C15  CTL2-0.18
 ATOM H15A HAL2 0.09
 ATOM H15B HAL2 0.09
 GROUP
 ATOM C16  CTL2-0.18
 ATOM H16A HAL2 0.09
 ATOM H16B HAL2 0.09
 GROUP
 ATOM C17  CTL1-0.09
 ATOM H17  HAL1 0.09
 GROUP
 ATOM C13  CTL1 0.00
 GROUP
 ATOM C18  CTL3-0.27  !methyl at c13
 ATOM H18A HAL3 0.09
 ATOM H18B HAL3 0.09
 ATOM H18C HAL3 0.09
 GROUP
 ATOM C12  CTL2-0.18
 ATOM H12A HAL2 0.09
 ATOM H12B HAL2 0.09
 GROUP
 ATOM C11  CTL2-0.18
 ATOM H11A HAL2 0.09
 ATOM H11B HAL2 0.09
 GROUP
 ATOM C9   CTL1-0.09
 ATOM H9   HAL1 0.09
 GROUP
 ATOM C10  CTL1 0.00
 GROUP
 ATOM C19  CTL3-0.27  !methyl at c10
 ATOM H19A HAL3 0.09
 ATOM H19B HAL3 0.09
 ATOM H19C HAL3 0.09
 GROUP
 ATOM C1   CTL2-0.18
 ATOM H1A  HAL2 0.09
 ATOM H1B  HAL2 0.09
 GROUP
 ATOM C2   CTL2-0.18
 ATOM H2A  HAL2 0.09
 ATOM H2B  HAL2 0.09
 GROUP
 ATOM C20  CTL2-0.09
 ATOM H20  HAL2 0.09
 GROUP
 ATOM C21  CTL3-0.27
 ATOM H21A HAL3 0.09
 ATOM H21B HAL3 0.09
 ATOM H21C HAL3 0.09
 GROUP
 ATOM C22  CTL2-0.18
 ATOM H22A HAL2 0.09
 ATOM H22B HAL2 0.09
 GROUP
 ATOM C23  CTL2-0.18
 ATOM H23A HAL2 0.09
 ATOM H23B HAL2 0.09
 GROUP
 ATOM C24  CTL2-0.18  !beyond this nomenclature may not be correct
 ATOM H24A HAL2 0.09
 ATOM H24B HAL2 0.09
 GROUP
 ATOM C25  CTL1-0.09  !c25
 ATOM H25  HAL1 0.09
 GROUP
 ATOM C26  CTL3-0.27  !terminal methyl, c26
 ATOM H26A HAL3 0.09
 ATOM H26B HAL3 0.09
 ATOM H26C HAL3 0.09
 GROUP
 ATOM C27  CTL3-0.27  !terminal methyl, c27
 ATOM H27A HAL3 0.09
 ATOM H27B HAL3 0.09
 ATOM H27C HAL3 0.09

 On Thu, Nov 6, 2014 at 7:16 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 11/6/14 8:38 AM, Venkat Reddy wrote:

  Dear Justin,
 Yes, the problem is with the blank line at the end of atomtypes.atp. Now
 its working fine. I have added the missing dihedral types from other
 sources.


  Thanks, I will fix that.

   I have compared the cholesterol CHARMM parameters that are converted to

 gromacs format and original parameters from
 toppar_all36_lipid_cholesterol.str file available in CHARMM website.
 I
 found some variations in the atom types.

 For eg., The atom type of  C3 atom from sterol ring in cholesterol is
 CTL1
 in CHARMM whereas it is CG311 in charmm36-Nov2014.ff.


  Which residue are you looking at?  There is no C3 atom with type CTL1
 in
 that stream file.  In any case, CG311 and CTL1 have identical parameters
 (see ffnonbonded.itp) since CG311 is used for CGenFF model compounds,
 which
 in the case of lipids, were just ported over and given unique types.
 Anything with a G as the second letter in the atom type is from CGenFF,
 indicating general to differentiate them from the main CHARMM types.


 -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

Re: [gmx-users] Charmm to gromacs conversion for lipids

[Venkat Reddy]

Dear Justin,
Please check the atom section of toppar_all36_lipid_cholesterol.str file
that I pasted below.

* Toppar stream file for cholesterol.  Stream following reading of
* top_all36_lipid.rtf  and par_all36_lipid.rtf

!reference
!Suits, F., Pitman, M., MacKerell, A.D., Jr., Feller, S.E. Molecular Level
!Organization of Saturated and Polyunsaturated Fatty Acids in a
!Phosphatidylcholine Bilayer Containing Cholesterol Submitted
!for publication

read rtf card append
* cholesterol residues
*

RESI CHL1  0.00  !cholesterol (name to avoid conflict with choline)
! atoms names correspond to the correct cholesterol nomenclature
GROUP
ATOM C3   CTL1 0.14
ATOM O3   OHL -0.66
ATOM H3'  HOL  0.43
ATOM H3   HAL1 0.09
GROUP
ATOM C4   CTL2-0.18
ATOM H4A  HAL2 0.09
ATOM H4B  HAL2 0.09
GROUP
ATOM C5   CEL1 0.00
ATOM C6   CEL1-0.15
ATOM H6   HEL1 0.15
GROUP
ATOM C7   CTL2-0.18
ATOM H7A  HAL2 0.09
ATOM H7B  HAL2 0.09
GROUP
ATOM C8   CTL1-0.09
ATOM H8   HAL1 0.09
GROUP
ATOM C14  CTL1-0.09
ATOM H14  HAL1 0.09
GROUP
ATOM C15  CTL2-0.18
ATOM H15A HAL2 0.09
ATOM H15B HAL2 0.09
GROUP
ATOM C16  CTL2-0.18
ATOM H16A HAL2 0.09
ATOM H16B HAL2 0.09
GROUP
ATOM C17  CTL1-0.09
ATOM H17  HAL1 0.09
GROUP
ATOM C13  CTL1 0.00
GROUP
ATOM C18  CTL3-0.27  !methyl at c13
ATOM H18A HAL3 0.09
ATOM H18B HAL3 0.09
ATOM H18C HAL3 0.09
GROUP
ATOM C12  CTL2-0.18
ATOM H12A HAL2 0.09
ATOM H12B HAL2 0.09
GROUP
ATOM C11  CTL2-0.18
ATOM H11A HAL2 0.09
ATOM H11B HAL2 0.09
GROUP
ATOM C9   CTL1-0.09
ATOM H9   HAL1 0.09
GROUP
ATOM C10  CTL1 0.00
GROUP
ATOM C19  CTL3-0.27  !methyl at c10
ATOM H19A HAL3 0.09
ATOM H19B HAL3 0.09
ATOM H19C HAL3 0.09
GROUP
ATOM C1   CTL2-0.18
ATOM H1A  HAL2 0.09
ATOM H1B  HAL2 0.09
GROUP
ATOM C2   CTL2-0.18
ATOM H2A  HAL2 0.09
ATOM H2B  HAL2 0.09
GROUP
ATOM C20  CTL2-0.09
ATOM H20  HAL2 0.09
GROUP
ATOM C21  CTL3-0.27
ATOM H21A HAL3 0.09
ATOM H21B HAL3 0.09
ATOM H21C HAL3 0.09
GROUP
ATOM C22  CTL2-0.18
ATOM H22A HAL2 0.09
ATOM H22B HAL2 0.09
GROUP
ATOM C23  CTL2-0.18
ATOM H23A HAL2 0.09
ATOM H23B HAL2 0.09
GROUP
ATOM C24  CTL2-0.18  !beyond this nomenclature may not be correct
ATOM H24A HAL2 0.09
ATOM H24B HAL2 0.09
GROUP
ATOM C25  CTL1-0.09  !c25
ATOM H25  HAL1 0.09
GROUP
ATOM C26  CTL3-0.27  !terminal methyl, c26
ATOM H26A HAL3 0.09
ATOM H26B HAL3 0.09
ATOM H26C HAL3 0.09
GROUP
ATOM C27  CTL3-0.27  !terminal methyl, c27
ATOM H27A HAL3 0.09
ATOM H27B HAL3 0.09
ATOM H27C HAL3 0.09

On Thu, Nov 6, 2014 at 7:16 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 11/6/14 8:38 AM, Venkat Reddy wrote:

 Dear Justin,
 Yes, the problem is with the blank line at the end of atomtypes.atp. Now
 its working fine. I have added the missing dihedral types from other
 sources.


 Thanks, I will fix that.

  I have compared the cholesterol CHARMM parameters that are converted to
 gromacs format and original parameters from
 toppar_all36_lipid_cholesterol.str file available in CHARMM website. I
 found some variations in the atom types.

 For eg., The atom type of  C3 atom from sterol ring in cholesterol is CTL1
 in CHARMM whereas it is CG311 in charmm36-Nov2014.ff.


 Which residue are you looking at?  There is no C3 atom with type CTL1 in
 that stream file.  In any case, CG311 and CTL1 have identical parameters
 (see ffnonbonded.itp) since CG311 is used for CGenFF model compounds, which
 in the case of lipids, were just ported over and given unique types.
 Anything with a G as the second letter in the atom type is from CGenFF,
 indicating general to differentiate them from the main CHARMM types.


 -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.




-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036
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Gromacs Users mailing list

* Please search the archive at 
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[gmx-users] Charmm to gromacs conversion for lipids

[Venkat Reddy]

Dear all,
I have a new lipid molecule and I want to simulate it using charmm36
forcefield. I have generated .str file using *paramchem* server and then
using the following command, I got the itp file.

./cgenff_charmm2gmx.py COL COL.mol2 COL.str charmm36.ff

Is this a reasonable approach for generating gromacs topology for a lipid
molecule? If I change the atom types in the generated itp file to lipid
atom types described in lipids.rtp, is it appropriate?

Thank you for your time

-- 
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 
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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Charmm to gromacs conversion for lipids

[Venkat Reddy]

Thank you Joao for the quick reply. My system has single lipid molecule and
I have pre- calculated charge information for every atom in the lipid. I
have edited charges on individual atoms apart from atom types.
By the way, Previous studies have reported a topology for same lipid but in
NAMD convention. Is there any other tool to convert NAMD to GROMACS
compatible format?

Thanks alot

On Wed, Nov 5, 2014 at 3:58 PM, João Martins joaomartins...@gmail.com
wrote:

 The rtp file is used by pdb2gmx for creating GROMACS topology and
 coordinate files. Changing it in the lipids.rtp will not do much other than
 allow you to generate from a pdb the .gro and .top for that molecule.
 Changing atom types is tricky and should be avoided in order to make sure
 you're using the cgenff-generated parameters, those atomtypes are connected
 to the molecule you submitted and the charmm36.ff used in the conversion.

 I'd advise against using cgenff-derived parameters for serious
 calculations, the charge penalties are usually pretty high and that means
 you won't have a realistic description of your system. However, if you
 really want to run a simulation using those parameters, that's perfectly
 possible. That command generates a usable topology and coordinate pair, as
 well as a parameter file that's loaded in the topology. For all intents and
 purposes, using those for a single molecule simulation will work and should
 be relatively straightforward. If you want to simulate a multi-molecule
 system, you can either manually create a coordinate file modifying the
 generated one or, alternatively, generate it using any molecule editing
 software, exporting a pdb and using pdb2gmx to generate a
 gromacs-compatible coordinate and topology file.



 *Joao Martins*

 joaomartins...@gmail.com

 On Wed, Nov 5, 2014 at 10:31 AM, Venkat Reddy venkat...@gmail.com wrote:

  Dear all,
  I have a new lipid molecule and I want to simulate it using charmm36
  forcefield. I have generated .str file using *paramchem* server and then
  using the following command, I got the itp file.
 
  ./cgenff_charmm2gmx.py COL COL.mol2 COL.str charmm36.ff
 
  Is this a reasonable approach for generating gromacs topology for a lipid
  molecule? If I change the atom types in the generated itp file to lipid
  atom types described in lipids.rtp, is it appropriate?
 
  Thank you for your time
 
  --
  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.
 
 --
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 * 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!

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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Charmm to gromacs conversion for lipids

[Venkat Reddy]

Dear Justin,
My lipid is cholesteryl oleate (CO). Since there are CHARMM36 parameters
available for cholesterol and oleate chain in POPC, I have clubbed both
together to generate the topology for CO (rtf file). Now I want to convert
this rtf to itp file. is there any shortcut to accomplish this task?

On Wed, Nov 5, 2014 at 5:57 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 11/5/14 7:03 AM, Venkat Reddy wrote:

 Thank you Joao for the quick reply. My system has single lipid molecule
 and
 I have pre- calculated charge information for every atom in the lipid. I
 have edited charges on individual atoms apart from atom types.
 By the way, Previous studies have reported a topology for same lipid but
 in
 NAMD convention. Is there any other tool to convert NAMD to GROMACS
 compatible format?


 You have to be careful here.  I would not use CGenFF for lipids, but for
 reasons different than what Joao was saying.  As is cautioned in the CGenFF
 description, you shouldn't use it for molecules for which a highly tuned
 biomolecular force field already covers much of, if not all, of the
 chemical space.  The CHARMM36 lipid force field is highly optimized and
 performs very well.  CGenFF, by its nature, is generalized.  With
 generalization and increased transferability comes a decrease in accuracy.
 Coupling charges calculated by a different method (is it compatible with
 what CHARMM normally requires, and are those charges tuned against the LJ
 parameters of the atom types to give reasonable intermolecular and
 water-water interactions?) with somewhat less accurate atom types and
 bonded parameters will probably lead to a poor result because you've got a
 hodge-podge of a topology.

 What is this lipid that you're trying to parametrize?  Are its functional
 groups covered by the existing parameters in the CHARMM36 lipid force
 field?  If they are, you should absolutely be using those parameters
 (charges, atom types, and bonded parameters).  Even small inaccuracies or
 imbalances can have a huge impact, especially on lipids, which are very
 sensitive.

 -Justin

 --
 ==

 Justin A. Lemkul, Ph.D.
 Ruth L. Kirschstein NRSA Postdoctoral Fellow

 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 629
 University of Maryland, Baltimore
 20 Penn St.
 Baltimore, MD 21201

 jalem...@outerbanks.umaryland.edu | (410) 706-7441
 http://mackerell.umaryland.edu/~jalemkul

 ==
 --
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-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036
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Re: [gmx-users] Charmm to gromacs conversion for lipids

[Venkat Reddy]

Thank you Justin for the tip. I have given .rtf file as input and the
script has generated me the desired output .itp file. The command I used is
as shown below.

./cgenff_charmm2gmx.py CHL1 CE-1.mol2 top_chol_ester.rtf
/usr/local/gromacs/share/gromacs/top/charmm36.ff


Thank you very much Justin for the help.

On Wed, Nov 5, 2014 at 6:05 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 11/5/14 7:33 AM, Venkat Reddy wrote:

 Dear Justin,
 My lipid is cholesteryl oleate (CO). Since there are CHARMM36 parameters
 available for cholesterol and oleate chain in POPC, I have clubbed both
 together to generate the topology for CO (rtf file). Now I want to convert
 this rtf to itp file. is there any shortcut to accomplish this task?


 In theory, our conversion script should handle that, because all the .str
 files are are .rtf and .prm entries, so if you don't have any new
 parameters, it can probably convert the .rtf itself.  Never tried it, but
 you can probably make it work.  Error messages are pretty descriptive in
 case of any issues.

 -Justin


  On Wed, Nov 5, 2014 at 5:57 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 11/5/14 7:03 AM, Venkat Reddy wrote:

  Thank you Joao for the quick reply. My system has single lipid molecule
 and
 I have pre- calculated charge information for every atom in the lipid. I
 have edited charges on individual atoms apart from atom types.
 By the way, Previous studies have reported a topology for same lipid but
 in
 NAMD convention. Is there any other tool to convert NAMD to GROMACS
 compatible format?


  You have to be careful here.  I would not use CGenFF for lipids, but
 for
 reasons different than what Joao was saying.  As is cautioned in the
 CGenFF
 description, you shouldn't use it for molecules for which a highly tuned
 biomolecular force field already covers much of, if not all, of the
 chemical space.  The CHARMM36 lipid force field is highly optimized and
 performs very well.  CGenFF, by its nature, is generalized.  With
 generalization and increased transferability comes a decrease in
 accuracy.
 Coupling charges calculated by a different method (is it compatible with
 what CHARMM normally requires, and are those charges tuned against the LJ
 parameters of the atom types to give reasonable intermolecular and
 water-water interactions?) with somewhat less accurate atom types and
 bonded parameters will probably lead to a poor result because you've got
 a
 hodge-podge of a topology.

 What is this lipid that you're trying to parametrize?  Are its functional
 groups covered by the existing parameters in the CHARMM36 lipid force
 field?  If they are, you should absolutely be using those parameters
 (charges, atom types, and bonded parameters).  Even small inaccuracies or
 imbalances can have a huge impact, especially on lipids, which are very
 sensitive.

 -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!

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 * 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.





 --
 ==

 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!

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 * 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
-- 
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Re: [gmx-users] Charmm to gromacs conversion for lipids

[Venkat Reddy]

Dear Justin,
While processing the lipid file using grompp, there was an error:

ERROR 1 [file chl1.itp, line 938]:
  No default Proper Dih. types


ERROR 2 [file chl1.itp, line 939]:
  No default Proper Dih. types


ERROR 3 [file chl1.itp, line 940]:
  No default Proper Dih. types


ERROR 4 [file chl1.itp, line 942]:
  No default Proper Dih. types


ERROR 5 [file chl1.itp, line 944]:
  No default Proper Dih. types


ERROR 6 [file chl1.itp, line 945]:
  No default Proper Dih. types


ERROR 7 [file chl1.itp, line 946]:
  No default Proper Dih. types


ERROR 8 [file chl1.itp, line 947]:
  No default Proper Dih. types


ERROR 9 [file chl1.itp, line 948]:
  No default Proper Dih. types


ERROR 10 [file chl1.itp, line 949]:
  No default Proper Dih. types


ERROR 11 [file chl1.itp, line 956]:
  No default Proper Dih. types


ERROR 12 [file chl1.itp, line 959]:
  No default Proper Dih. types


I quickly went through the itp file and found atom types CEL1 and CTL1 as a
part of dihedral are troubling. I have checked the parent rtf file for the
dihedral definition of these atoms. The dihedral was defined as

 C3 C4 C5 C10 1.5367 111.70 54.04 115.09 1.5304

How to mention this information in ffbonded.itp?

Thank you for your valuable time.

On Wed, Nov 5, 2014 at 6:16 PM, Venkat Reddy venkat...@gmail.com wrote:

 Thank you Justin for the tip. I have given .rtf file as input and the
 script has generated me the desired output .itp file. The command I used is
 as shown below.

 ./cgenff_charmm2gmx.py CHL1 CE-1.mol2 top_chol_ester.rtf
 /usr/local/gromacs/share/gromacs/top/charmm36.ff


 Thank you very much Justin for the help.

 On Wed, Nov 5, 2014 at 6:05 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 11/5/14 7:33 AM, Venkat Reddy wrote:

 Dear Justin,
 My lipid is cholesteryl oleate (CO). Since there are CHARMM36 parameters
 available for cholesterol and oleate chain in POPC, I have clubbed both
 together to generate the topology for CO (rtf file). Now I want to
 convert
 this rtf to itp file. is there any shortcut to accomplish this task?


 In theory, our conversion script should handle that, because all the .str
 files are are .rtf and .prm entries, so if you don't have any new
 parameters, it can probably convert the .rtf itself.  Never tried it, but
 you can probably make it work.  Error messages are pretty descriptive in
 case of any issues.

 -Justin


  On Wed, Nov 5, 2014 at 5:57 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 11/5/14 7:03 AM, Venkat Reddy wrote:

  Thank you Joao for the quick reply. My system has single lipid molecule
 and
 I have pre- calculated charge information for every atom in the lipid.
 I
 have edited charges on individual atoms apart from atom types.
 By the way, Previous studies have reported a topology for same lipid
 but
 in
 NAMD convention. Is there any other tool to convert NAMD to GROMACS
 compatible format?


  You have to be careful here.  I would not use CGenFF for lipids, but
 for
 reasons different than what Joao was saying.  As is cautioned in the
 CGenFF
 description, you shouldn't use it for molecules for which a highly tuned
 biomolecular force field already covers much of, if not all, of the
 chemical space.  The CHARMM36 lipid force field is highly optimized and
 performs very well.  CGenFF, by its nature, is generalized.  With
 generalization and increased transferability comes a decrease in
 accuracy.
 Coupling charges calculated by a different method (is it compatible with
 what CHARMM normally requires, and are those charges tuned against the
 LJ
 parameters of the atom types to give reasonable intermolecular and
 water-water interactions?) with somewhat less accurate atom types and
 bonded parameters will probably lead to a poor result because you've
 got a
 hodge-podge of a topology.

 What is this lipid that you're trying to parametrize?  Are its
 functional
 groups covered by the existing parameters in the CHARMM36 lipid force
 field?  If they are, you should absolutely be using those parameters
 (charges, atom types, and bonded parameters).  Even small inaccuracies
 or
 imbalances can have a huge impact, especially on lipids, which are very
 sensitive.

 -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!

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 send a mail to gmx-users-requ...@gromacs.org

[gmx-users] Coordination vs cumulative number in g_rdf

[Venkat Reddy]

Dear Gromacs users

Is the cumulative number obtained using the -cn flag with g_rdf same as
coordination number? If not, then how can I calculate coordination number
from cumulative number?

Thanks

-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036
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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Charmm to gromacs conversion for lipids

[Venkat Reddy]

Dear Justin,
Thanks for the update. But unfortunately I couldn't find the parameters for
cholesteryl oleate. So, I tried to convert again the parameters from CHARMM
to GROMACS using these updated files:

./cgenff_charmm2gmx.py CHL1 CE-1.mol2 top_chol_ester.rtf
/usr/local/gromacs/share/gromacs/top/charmm36-nov2014.ff

Here I am getting an error like,

Traceback (most recent call last):
  File ./cgenff_charmm2gmx.py, line 778, in module
atomtypes = read_gmx_atomtypes(atomtypes_filename)
  File ./cgenff_charmm2gmx.py, line 71, in read_gmx_atomtypes
var = [entry[0],entry[1]]
IndexError: list index out of range

If I use the charmm36 files uploaded in March 2014, Its not throwing any
error. Is there something wrong in the updated files?


On Thu, Nov 6, 2014 at 6:09 AM, Justin Lemkul jalem...@vt.edu wrote:



 On 11/5/14 10:23 AM, Venkat Reddy wrote:

 Dear Justin,

 While processing the lipid file using grompp, there was an error:

 ERROR 1 [file chl1.itp, line 938]:
No default Proper Dih. types


 ERROR 2 [file chl1.itp, line 939]:
No default Proper Dih. types


 ERROR 3 [file chl1.itp, line 940]:
No default Proper Dih. types


 ERROR 4 [file chl1.itp, line 942]:
No default Proper Dih. types


 ERROR 5 [file chl1.itp, line 944]:
No default Proper Dih. types


 ERROR 6 [file chl1.itp, line 945]:
No default Proper Dih. types


 ERROR 7 [file chl1.itp, line 946]:
No default Proper Dih. types


 ERROR 8 [file chl1.itp, line 947]:
No default Proper Dih. types


 ERROR 9 [file chl1.itp, line 948]:
No default Proper Dih. types


 ERROR 10 [file chl1.itp, line 949]:
No default Proper Dih. types


 ERROR 11 [file chl1.itp, line 956]:
No default Proper Dih. types


 ERROR 12 [file chl1.itp, line 959]:
No default Proper Dih. types


 I quickly went through the itp file and found atom types CEL1 and CTL1 as
 a
 part of dihedral are troubling. I have checked the parent rtf file for the
 dihedral definition of these atoms. The dihedral was defined as

   C3 C4 C5 C10 1.5367 111.70 54.04 115.09 1.5304

 How to mention this information in ffbonded.itp?


 Parameters should be specified by atom type, not atom name.  Regardless,
 you can always add parameters to [dihedraltypes] in ffbonded.itp after unit
 conversion.  Try the latest CHARMM36 force field files, which I just
 uploaded today:

 http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs

 I added a bunch of lipids and associated parameters that people had asked
 for. Maybe what you need is already included there.

 -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!

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 * 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

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[gmx-users] Regarding spatial distribution data analysis

[Venkat Reddy]

 Dear Gromacs users

I obtained two sets of data for the spatial distribution of solvent around
solute in two different systems using g_spatial. I want to visualize the
data using isosurface mode in vmd. The data range for both the sets are
different. How do I compare the solvent distribution in both the systems?
For example if I set the data range in vmd to say 0 to 20 in both sets
(where the full range for set 1 is say 0 to 120 and that for set 2 is 0 to
80) am I making a meaningful comparison?

Thanks

-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036
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[gmx-users] Simulating beta-peptides

[Venkat Reddy]

Dear Gromacs users,
Can I use GROMOS53A6 ff for simulating beta-peptides? I found some articles
on beta peptide simulations using GROMOS53A6 and 53A7 ff. Do I have to edit
any  dihedral angle info to process my beta peptide after pdb2gmx step?

Thank you for the concern

Venkat
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[gmx-users] Regarding 'insolidangle' and some tools

[Venkat Reddy]

Dear Teemu,

I have been following one of your presentations on Improved Gromacs
analysis using dynamic selections and also referring your publication on
LDL modeling and dynamics. My simulation system is quite similar to your
LDL model. In your presentation I came across the following dynamic
selection.

underprot = insolidangle center com of lipids span group Protein cutoff 5;

I know the purpose of the above statement but I didn't get the meaning of
some of the words, like insolidangle and cutoff=5. If don't mind, can
you please explain this statement?

There are some useful tools for spherical systems like g_jumpdist, g_rdf
(modified)etc that you explained in your presentation. Do you have any
modified gromacs copy with the inclusion of these tools. Because these
tools are very important for my system. Sorry for such a lengthy mail.

Thank you for your time and concern

Venkat
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Re: [gmx-users] Regarding 'insolidangle' and some tools

[Venkat Reddy]

Thank you Sir. gmx help explains it. I tried to compile the tools on
gromacs-4.5 but somehow the installation was terminating with errors. Then
I thought, you might have the modified gromacs copy. Anyway, I will try to
install the tools on gromacs-4.5 template. Thank you sir for your time and
concern.


On Thu, Jul 10, 2014 at 9:51 AM, Teemu Murtola teemu.murt...@gmail.com
wrote:

 Hi,


 On Wed, Jul 9, 2014 at 7:13 PM, Venkat Reddy venkat...@gmail.com wrote:

  underprot = insolidangle center com of lipids span group Protein cutoff
  5;
 
  I know the purpose of the above statement but I didn't get the meaning of
  some of the words, like insolidangle and cutoff=5. If don't mind, can
  you please explain this statement?
 

 Please see 'gmx help selections keywords insolidangle' for a general
 explanation. If that is not clear, I can clarify that further.

 There are some useful tools for spherical systems like g_jumpdist, g_rdf
  (modified)etc that you explained in your presentation. Do you have
 any
  modified gromacs copy with the inclusion of these tools. Because these
  tools are very important for my system. Sorry for such a lengthy mail.
 

 I have sent whatever I had for these tools to you personally in May 2013.
 Not much has happened since, except that 'gmx distance', 'gmx gangle' and
 'gmx sasa' may be able to cover some parts of the needs. Due to various
 reasons (most important of which is that I have left academia in 2010), it
 has not been exactly fast to get any of those tools actually included in
 Gromacs.

 I never had modified Gromacs copy, but only a set of tools and the
 selection engine that could be compiled against an existing Gromacs
 installation. The selection engine was included in Gromacs 4.5, and the
 code has changed a lot since, but the tools have not been updated and so do
 not work with newer Gromacs versions without modifications.
 --
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-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036
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Re: [gmx-users] Regarding lipid topology

[Venkat Reddy]

Dear Sir,
I have measured the dihedral angles for both cis and trans conformations
using VMD. As expected, for cis isomer the dihedral angle was 0 and for
trans = 180. Expect this, I couldn't find any change between these isomers.


On Thu, Jul 3, 2014 at 3:07 PM, Dr. Vitaly Chaban vvcha...@gmail.com
wrote:

 Unlikely anything on top of dihedrals.

 Try to use VMD to see if the lipid molecules look as you like.

 I do not have to handle lipid isomer simulations, fortunately.


 Dr. Vitaly V. Chaban


 On Wed, Jul 2, 2014 at 7:33 PM, Venkat Reddy venkat...@gmail.com wrote:
  Thank you Sir. Sorry for the late reply. So, the changes like dihedral
  angle for C8-C9=C10-C11 should be 180 instead of 0 in trans state. Are
  there any other adjustments I should make to build the trans lipid isomer
  topology from cis? Thank you for your valuable time and concern.
 
 
  On Mon, Jun 16, 2014 at 4:44 PM, Dr. Vitaly Chaban vvcha...@gmail.com
  wrote:
 
  Of course, no. You need to adjust your topology (force field?) to
  distinguish between cis- and trans- states.
 
 
  Dr. Vitaly V. Chaban
 
 
  On Mon, Jun 16, 2014 at 11:03 AM, Venkat Reddy venkat...@gmail.com
  wrote:
   Dear all,
   I want to simulate a membrane protein system. My membrane is composed
 of
   DOPC (cis isomer) and DEPC (trans isomer). I have downloaded DOPC
  topology
   from lipidbook website. Since DOPC and DEPC are isomers, can I use the
   topology of DOPC for DEPC also?
  
   Thank and regards
  
   Venkat Reddy Chirasani
   PhD student
   Laboratory of Computational Biophysics
   Department of Biotechnology
   IIT Madras
   Chennai
   INDIA-600036
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   Gromacs Users mailing list
  
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  --
  With Best Wishes
  Venkat Reddy Chirasani
  PhD student
  Laboratory of Computational Biophysics
  Department of Biotechnology
  IIT Madras
  Chennai
  INDIA-600036
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-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036
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Re: [gmx-users] problem with calculating angles and dynamic selections

[Venkat Reddy]

Hi,
Have you tried gmx gangle -g1 vector -g2 vector -group1 resname RES and
name A B -group2 resname RES and name A C

I have valid results using the above command. In fact, I didn't find any
problem with -g1 angle also.


On Thu, Jul 3, 2014 at 7:42 PM, gigo g...@ibb.waw.pl wrote:

 Hi!
 I find it impossible to calculate (some) angles between atoms using
 dynamic selection in 'gmx gangle' command. The problem is, that the dynamic
 selection mechanism persistently sorts numbers of atoms specified in the
 input. So, if I have atoms A, B and C with ascending indexes, I am not able
 to calculate angle B-A-C - I only get value for A-B-C, no matter how I
 order them in the command line. Is there any way to do it without writing
 an index file (which I have to parse anyway, because the same mechanism
 sorts atoms in 'gmx select'...)? If not, I will submit a feature request on
 redmine - something like -nosort option...
 Regards,

 Grzegorz Wieczorek
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Venkat Reddy Chirasani
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Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
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INDIA-600036
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Re: [gmx-users] problem with calculating angles and dynamic selections

[Venkat Reddy]

Hi,
I have tried gmx gangle -g1 angle option. Its sorting the atoms specified
in the input. I think it might be a bug. gmx gangle  -g1 vector -g2 vector
is doing fine.


On Thu, Jul 3, 2014 at 7:42 PM, gigo g...@ibb.waw.pl wrote:

 Hi!
 I find it impossible to calculate (some) angles between atoms using
 dynamic selection in 'gmx gangle' command. The problem is, that the dynamic
 selection mechanism persistently sorts numbers of atoms specified in the
 input. So, if I have atoms A, B and C with ascending indexes, I am not able
 to calculate angle B-A-C - I only get value for A-B-C, no matter how I
 order them in the command line. Is there any way to do it without writing
 an index file (which I have to parse anyway, because the same mechanism
 sorts atoms in 'gmx select'...)? If not, I will submit a feature request on
 redmine - something like -nosort option...
 Regards,

 Grzegorz Wieczorek
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Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036
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Re: [gmx-users] Regarding lipid topology

[Venkat Reddy]

Thank you Sir. Sorry for the late reply. So, the changes like dihedral
angle for C8-C9=C10-C11 should be 180 instead of 0 in trans state. Are
there any other adjustments I should make to build the trans lipid isomer
topology from cis? Thank you for your valuable time and concern.


On Mon, Jun 16, 2014 at 4:44 PM, Dr. Vitaly Chaban vvcha...@gmail.com
wrote:

 Of course, no. You need to adjust your topology (force field?) to
 distinguish between cis- and trans- states.


 Dr. Vitaly V. Chaban


 On Mon, Jun 16, 2014 at 11:03 AM, Venkat Reddy venkat...@gmail.com
 wrote:
  Dear all,
  I want to simulate a membrane protein system. My membrane is composed of
  DOPC (cis isomer) and DEPC (trans isomer). I have downloaded DOPC
 topology
  from lipidbook website. Since DOPC and DEPC are isomers, can I use the
  topology of DOPC for DEPC also?
 
  Thank and regards
 
  Venkat Reddy Chirasani
  PhD student
  Laboratory of Computational Biophysics
  Department of Biotechnology
  IIT Madras
  Chennai
  INDIA-600036
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Venkat Reddy Chirasani
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Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
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INDIA-600036
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Re: [gmx-users] grompp

[Venkat Reddy]

Hi,
Did you update the 2nd line of your gro file (sol.gro) after adding ligand
coordinates?


On Wed, Jun 18, 2014 at 12:32 PM, Meenakshi Rajput ashi.rajpu...@gmail.com
wrote:

 Hi gromacs users
 I run the grompp command
 (grompp_d -v -f minim.mdp -c sol.gro -o min.tpr -p hsa.top)
  to generate .tpr file but i got the following error
 Fatal error:
 number of coordinates in coordinate file (sol.gro, 140012)
  does not match topology (hsa.top, 140027)
 When I opened gro file, only protein and sol molecules are seen in .gro
 file but no ligand molecules. I dont know why it is happening..
 Can anybody help me?
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Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036
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[gmx-users] Regarding lipid topology

[Venkat Reddy]

Dear all,
I want to simulate a membrane protein system. My membrane is composed of
DOPC (cis isomer) and DEPC (trans isomer). I have downloaded DOPC topology
from lipidbook website. Since DOPC and DEPC are isomers, can I use the
topology of DOPC for DEPC also?

Thank and regards

Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036
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Re: [gmx-users] Regarding membrane construction

[Venkat Reddy]

Dear Justin,
I am following membrane-protein tutorial to construct my system. During
equilibration and production MD, I am receiving the following NOTES.

NOTE 1 [file md.mdp]:
  nstcomm  nstcalcenergy defeats the purpose of nstcalcenergy, setting
  nstcomm to nstcalcenergy


NOTE 2 [file md.mdp]:
  leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1

I have downloaded the mdp files from tutorial. Is it ok if I omit these
notes and carry the production run?


On Tue, Jun 10, 2014 at 5:41 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 6/10/14, 1:12 AM, Venkat Reddy wrote:

 I have used
 editconf -f protein.gro -c -bt cubic -d 1.5 -o confout.gro
 to set the box.

 Then
 genbox -cp confout.gro -cs dppc128.gro -o protein_in_membrane.gro
 got hanged


 Am I missing something here???


 Don't extend the z-dimension at this stage.  You want to expand the
 membrane laterally (along x and y, usually), so set the box vectors
 manually with editconf -box, not -d (though using -d can tell you what
 suitable vectors in x and y might be).  You can always increase the
 z-dimension, if you need to, later using editconf and then fill with water
 using genbox in a separate step.


 -Justin

 --
 ==

 Justin A. Lemkul, Ph.D.
 Ruth L. Kirschstein NRSA 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
 http://mackerell.umaryland.edu/~jalemkul

 ==
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Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036
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Re: [gmx-users] Regarding membrane construction

[Venkat Reddy]

Thank you Chen for the quick reply. I will try both options.


On Mon, Jun 9, 2014 at 12:52 PM, 陈功 gchen...@gmail.com wrote:

 Dear Venkat,
 I guess there are some other methods to generate  new lipid bilayer
 construct by using genbox -cp your_membrane_protein -ci lipid_monomer -nmol
 xxxcalculate by yourself -try 1000 -cs solovents.gro -p top.top -o
 new_conf.gro or using editconf  cat ...Another way, you can try the script
 packmol. Be more patient.  haha, I m also a new gmx user.
 Good  luck,
 chen gong






 From: Venkat Reddy
 Date: 2014-06-09 15:31
 To: Discussion list for GROMACS users
 Subject: [gmx-users] Regarding membrane construction
 Dear all,
 I am studying a membrane protein of length 288 residues. I want to simulate
 in a DPPC bilayer. I have downloaded dppc equilibrated bilayer from Peter
 Tieleman's website as directed by Justin in his membrane-protein tutorial.
 But I found 128 lipid membrane is not enough for my protein. From the
 literature, I found I need  81 lipids in each leaflet. How can I construct
 a 162 lipid equilibrated bilayer? I tried CHARMM-GUI to build it. But the
 equilibration is giving RATTLE error. Please help me in this regard.

 Thank you

 Venkat
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PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036
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Re: [gmx-users] Problem in NVT equilibration

[Venkat Reddy]

Dear Surinarayanan,
You have to create appropriate index file by grouping solvent and solute
molecules separately (eg: Protein_ligand_membrane  Water_and_ions).


On Mon, Jun 9, 2014 at 12:33 PM, Balasubramanian Suriyanarayanan 
bsns...@gmail.com wrote:

 Dear User
  I do a protein ligand simulation in a lipid environment.  When I do NVT
 equilibration I get an error message saying 32 molecules are not part of
 any coupling groups.

 Do I need to change the .mdp file.

 Please clarify.

 Regards

 Surinarayanan
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Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036
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Re: [gmx-users] Problem in NVT equilibration

[Venkat Reddy]

Hi,
No need to group SOL and ions. They will default present in index group as
Water_and_ions. Just mention Water_and_ions in your mdp file.


On Mon, Jun 9, 2014 at 5:26 PM, Balasubramanian Suriyanarayanan 
bsns...@gmail.com wrote:

 Sir, Thanks for your reply.

 I really works. But the next error message was Group SOL_CL not found in
 indexfile.
 Maybe you have non-default goups in your .mdp file, while not using the
 '-n' option of grompp.
 In that case use the '-n' option

  But I have really used -n option.


 regards

 Suriyanarayanan



 On Mon, Jun 9, 2014 at 3:00 PM, Venkat Reddy venkat...@gmail.com wrote:

  Dear Surinarayanan,
  You have to create appropriate index file by grouping solvent and solute
  molecules separately (eg: Protein_ligand_membrane  Water_and_ions).
 
 
  On Mon, Jun 9, 2014 at 12:33 PM, Balasubramanian Suriyanarayanan 
  bsns...@gmail.com wrote:
 
   Dear User
I do a protein ligand simulation in a lipid environment.  When I do
 NVT
   equilibration I get an error message saying 32 molecules are not part
 of
   any coupling groups.
  
   Do I need to change the .mdp file.
  
   Please clarify.
  
   Regards
  
   Surinarayanan
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  --
  With Best Wishes
  Venkat Reddy Chirasani
  PhD student
  Laboratory of Computational Biophysics
  Department of Biotechnology
  IIT Madras
  Chennai
  INDIA-600036
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Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036
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Re: [gmx-users] Regarding membrane construction

[Venkat Reddy]

Thank you Justin.


On Mon, Jun 9, 2014 at 5:28 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 6/9/14, 3:22 AM, 陈功 wrote:

 Dear Venkat, I guess there are some other methods to generate  new lipid
 bilayer construct by using genbox -cp your_membrane_protein -ci
 lipid_monomer
 -nmol xxxcalculate by yourself -try 1000 -cs solovents.gro -p top.top -o
 new_conf.gro or using editconf  cat ...Another way, you can try the
 script
 packmol. Be more patient.  haha, I m also a new gmx user. Good  luck, chen


 Packmol is a good choice, but the approach above with genbox likely won't
 work.  It will produce a random insertion of lipids.  The simplest way
 within Gromacs to create a membrane of sufficient size is to place the
 protein in a suitably sized box (with editconf) and then

 genbox -cp protein.gro -cs membrane.gro -o protein_in_membrane.gro

 -Justin

 --
 ==

 Justin A. Lemkul, Ph.D.
 Ruth L. Kirschstein NRSA 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
 http://mackerell.umaryland.edu/~jalemkul

 ==

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-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036
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Re: [gmx-users] Regarding membrane construction

[Venkat Reddy]

Dear Justin,
I have tried the command
genbox -cp protein.gro -cs membrane.gro -o protein_in_membrane.gro
 but it got hanged. Is there something wrong with the command?


On Mon, Jun 9, 2014 at 5:50 PM, 陈功 gchen...@gmail.com wrote:

 Thanks for correction. i appriciate it :)
 Chen Gong





 From: Justin Lemkul
 Date: 2014-06-09 19:58
 To: gmx-users
 Subject: Re: [gmx-users] Regarding membrane construction


 On 6/9/14, 3:22 AM, 陈功 wrote:
  Dear Venkat, I guess there are some other methods to generate  new lipid
  bilayer construct by using genbox -cp your_membrane_protein -ci
 lipid_monomer
  -nmol xxxcalculate by yourself -try 1000 -cs solovents.gro -p top.top -o
  new_conf.gro or using editconf  cat ...Another way, you can try the
 script
  packmol. Be more patient.  haha, I m also a new gmx user. Good  luck,
 chen

 Packmol is a good choice, but the approach above with genbox likely won't
 work.
   It will produce a random insertion of lipids.  The simplest way within
 Gromacs
 to create a membrane of sufficient size is to place the protein in a
 suitably
 sized box (with editconf) and then

 genbox -cp protein.gro -cs membrane.gro -o protein_in_membrane.gro

 -Justin

 --
 ==

 Justin A. Lemkul, Ph.D.
 Ruth L. Kirschstein NRSA 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
 http://mackerell.umaryland.edu/~jalemkul

 ==
 --
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Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036
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Re: [gmx-users] Regarding membrane construction

[Venkat Reddy]

I have used
editconf -f protein.gro -c -bt cubic -d 1.5 -o confout.gro
to set the box.

Then
genbox -cp confout.gro -cs dppc128.gro -o protein_in_membrane.gro
got hanged


Am I missing something here???


On Tue, Jun 10, 2014 at 2:51 AM, Justin Lemkul jalem...@vt.edu wrote:



 On 6/9/14, 9:08 AM, Venkat Reddy wrote:

 Dear Justin,
 I have tried the command
 genbox -cp protein.gro -cs membrane.gro -o protein_in_membrane.gro
   but it got hanged. Is there something wrong with the command?


 I wouldn't expect a hang as long as the box is set to appropriate
 dimensions. The new box for the protein shouldn't be substantially larger
 than the membrane itself.


 -Justin

 --
 ==

 Justin A. Lemkul, Ph.D.
 Ruth L. Kirschstein NRSA 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
 http://mackerell.umaryland.edu/~jalemkul

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Department of Biotechnology
IIT Madras
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Re: [gmx-users] (no subject)

[Venkat Reddy]

Hi,
Did you modify your forcefield such a way that it applicable for lipid
atoms also???
If not, follow Justin's tutorial
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/02_topology.html


On Tue, Jun 10, 2014 at 10:31 AM, Balasubramanian Suriyanarayanan 
bsns...@gmail.com wrote:

 Dear users,

  In a lipid membrane simulation  Grompp command gives me a error  atom
 LC# not found. What do I need to change?

 regards
  Suriyanarayanan
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Department of Biotechnology
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Re: [gmx-users] counter ions in coarse grained simulations

[Venkat Reddy]

Hi Neha,
You can simply add ions using genion. Its similar to what we do in AA
system. You have to append #include martini_v2.0_ions.itp to your .top
file.


On Fri, May 23, 2014 at 6:17 AM, Neha Gandhi n.gandh...@gmail.com wrote:

 Hi List,

 My query is not really related to gromacs but I appreciate response from
 people who might have tried using coarse grained simualtions using Martini
 force field in gromacs.

 I haven't come across tutorial or mailing list where people have added
 counter ions to a coarse grained protein system. Do we also coarse grained
 counter-ions ? or Do I assume that some sort of potential will take care of
 the effect? Or are the parameters from atomistic force fields are retained
 for counter-ions?

 How do I add counter-ions in gromacs to coarse grained topology?

 Your feedback is appreciated.

 Regards,
 Neha
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Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036
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Re: [gmx-users] Units of Gibbs free energy from g_sham

[Venkat Reddy]

Thank you Justin for the quick reply.


On Thu, May 1, 2014 at 3:15 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 5/1/14, 5:38 AM, Venkat Reddy wrote:

 Dear all,
 What is the unit of dG calculated from g_sham? Is it J/K/mol or KJ/K/mol?


 Neither.  It's kJ/mol, as printed in the output .xpm file.

 -Justin

 --
 ==

 Justin A. Lemkul, Ph.D.
 Ruth L. Kirschstein NRSA 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
 http://mackerell.umaryland.edu/~jalemkul

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Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
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INDIA-600036
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Re: [gmx-users] Fwd: Concatenating two trajectories

[Venkat Reddy]

No, By default it will give the starting time from where it started. I
doubt your simulation extension has some problem. The commands to extend  a
simulation are
tpbconv -s old.tpr -extend time in ps -o new.tpr
mdrun -v -s new.tpr -cpi state.cpt -deffnm new

Hope it will help you.


On Tue, Apr 22, 2014 at 11:00 AM, Sunita sunita@gmail.com wrote:

 Hello Venkat,

 Yeah, I think by default it will give 0 ps as start time for both
 trajectories and it should be set by user using -settime flag
 Correct me if I am wrong.

 Regards

 --
 View this message in context:
 http://gromacs.5086.x6.nabble.com/Fwd-Concatenating-two-trajectories-tp5015956p5015992.html
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Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036
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Re: [gmx-users] Fwd: Concatenating two trajectories

[Venkat Reddy]

Hi,
First of all, are you sure that you extended 2.xtc from 40ns?

Can you post your trjcat output, which shows the starting frame of each
trajectory.

It should be like as shown below

Summary of files and start times used:

  FileStart time   Time step
-
  1.xtc0.000 ps2.000 ps
  2.xtc 4.000 ps2.000 ps



On Mon, Apr 21, 2014 at 11:42 AM, Sunita sunita@gmail.com wrote:

 Thanks for quick response..
 I tried trjcat -f 1.xtc 2.xtc -o concatenate.xtc
 But its not concatenating the two, rather overwriting the 2nd trajectory to
 1st one. There should be 1600 frames but output contains only 800 frames.

 Thanks

 --
 View this message in context:
 http://gromacs.5086.x6.nabble.com/Fwd-Concatenating-two-trajectories-tp5015956p5015958.html
 Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036
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Re: [gmx-users] Fwd: Concatenating two trajectories

[Venkat Reddy]

So, that is the problem. Your second trajectory also has the same start
time. Some how you didn't extend your second run from where your 1st run
has finished.

Out of curiosity, why is your time step 50ps? Its too big for a simulation.
Generally it should be 2fs.


On Mon, Apr 21, 2014 at 12:30 PM, Sunita sunita@gmail.com wrote:

 Hello Venkat,

 Ya, I am sure that I use 1st.cpt to run next 40 ns job
  Find below the output of trjcat

 Summary of files and start times used:

   FileStart time   Time step
 -
 complex_prod1_old.xtc0.000 ps   50.000 ps
 complex_prod1.xtc0.000 ps   50.000 ps WARNING: same
 Start time as previous

 Thanks

 --
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 Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
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INDIA-600036
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Re: [gmx-users] Fwd: Concatenating two trajectories

[Venkat Reddy]

Hi Tsjerk,
Sorry for the confusion. I thought its time step which is actually
output writing frequency. Thank you sir for the correction.


On Mon, Apr 21, 2014 at 2:39 PM, Tsjerk Wassenaar tsje...@gmail.com wrote:

 Hi Venkat,

 That time step is the time step in the output trajectory. Yours said 2.000
 ps, not fs.

 Cheers,

 Tsjerk
 On Apr 21, 2014 9:35 AM, Venkat Reddy venkat...@gmail.com wrote:

  So, that is the problem. Your second trajectory also has the same start
  time. Some how you didn't extend your second run from where your 1st run
  has finished.
 
  Out of curiosity, why is your time step 50ps? Its too big for a
 simulation.
  Generally it should be 2fs.
 
 
  On Mon, Apr 21, 2014 at 12:30 PM, Sunita sunita@gmail.com wrote:
 
   Hello Venkat,
  
   Ya, I am sure that I use 1st.cpt to run next 40 ns job
Find below the output of trjcat
  
   Summary of files and start times used:
  
 FileStart time   Time step
   -
   complex_prod1_old.xtc0.000 ps   50.000 ps
   complex_prod1.xtc0.000 ps   50.000 ps WARNING: same
   Start time as previous
  
   Thanks
  
   --
   View this message in context:
  
 
 http://gromacs.5086.x6.nabble.com/Fwd-Concatenating-two-trajectories-tp5015956p5015962.html
   Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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  --
  With Best Wishes
  Venkat Reddy Chirasani
  PhD student
  Laboratory of Computational Biophysics
  Department of Biotechnology
  IIT Madras
  Chennai
  INDIA-600036
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PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036
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Re: [gmx-users] Fwd: Concatenating two trajectories

[Venkat Reddy]

Hi,
As far as I know, trjcat -f 1.xtc 2.xtc -o combined.xtc is enough to
concatenate two xtc files. No need to give any extra options (-cat or
-settime).


On Mon, Apr 21, 2014 at 11:02 AM, sunita gupta sunita@gmail.com wrote:

 Hello Everyone,


 I have two trajectories of 40 ns each, the first one is from 0 to 40 ns and
 next one is extended to next 40 ns taking .cpt file of the first
  I concatenating the two using two commands:
 1. trjcat -f 1st.xtc 2nd.xtc -o combine1.xtc -cat
 2. trjcat -f 1st.xtc 2nd.xtc -o combine2.xtc -settime (selecting 0.000 ps
 for 1st and 4 ps for 2nd)

 But when I plotted the rmsd using combine1.xtc and combine2.xtc I am
 getting very strange plots

 Unfortunately I am not able to post the plots as its saying msg is too big
 to be posted and bouncing back...
 Can anyone suggest me whats wrong with this method.





 Best Regards
 --
 SUNITA GUPTA
 Senior Research Fellow
 Bioinformatics Centre
 Jawaharlal Nehru University
 New Delhi- 110067
 Email- sunita@gmail.com





 --
 --
 SUNITA GUPTA
 Senior Research Fellow
 Bioinformatics Centre
 Jawaharlal Nehru University
 New Delhi- 110067
 Email- sunita@gmail.com
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Department of Biotechnology
IIT Madras
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