from:"Neha Gandhi"

[gmx-users] multiple nodes

2020-04-27 Thread Neha Gandhi

Dear List,
Below is the job script for running gromacs on our HPC (single node)

#!/bin/bash -l
#PBS -N gro1
#PBS -l walltime=300:00:00
#PBS -l select=3:ncpus=12:mpiprocs=12:mem=32gb
#PBS -j oe

cd $PBS_O_WORKDIR

module purge
module load gromacs/2019.3-foss-2019a
export OMP_NUM_THREADS=12
gmx_mpi mdrun -v -deffnm step4.1_equilibration

Could you help with the job script for multiple nodes? Do I need mpirun -np
24 gmx_mpi... in the syntax?

Thanks for your help in advance.

Regards,
Neha






-- 
Regards,
Dr. Neha S. Gandhi,
Vice Chancellor's Research Fellow,
Queensland University of Technology,
2 George Street, Brisbane, QLD 4000
Australia
LinkedIn
Research Gate
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[gmx-users] Equilibration using position restraints in NPT

2017-10-08 Thread Neha Gandhi

Thank you Mark.

The nanotube is 2x2x13 nm long. Then I use editconf with -c  and -d  2 and
solvate using spc216.gro.

How can I calculate box size after NVT so that I get density of 1 or 0.99
when using pressure coupling?





> Message: 1
> Date: Sun, 8 Oct 2017 23:38:58 +1000
> From: Neha Gandhi <n.gandh...@gmail.com>
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] Equilibration using position restraints in NPT
> Message-ID:
> <CA+Hq8HyXsHSXfNAe5AmBmy3ArxS-=aZHJckdJSC4yqWUMJDbmA@mail.
> gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> This is a very common post on previous mailing list however, I am still not
> able to fix the problem of position restraints during NPT.
>
> I have a carbon nanotube aligned to z-direction. I am trying to simulate
> infinite nanotube using periodic conditions. It is common to use position
> restraints for nanotube (most papers report this). I have imposed position
> restraints on nanotube and in doing so, the coordinates fluctuates by 0.5-1
> nm. This is not an issue with NVT simulation (Berendsen thermostat and
> barostat). I tried different thermostats and barostats, they deform the
> nanotube as previously discussed on gromacs mailing list.
>
> How do I equilibrate nanotube system with position restraints when used
> together with pressure coupling? Should I play with the box size after
> first NVT run?
> The force field is opls based on gromacs guideline on CNTs and GROMACS
> version is 5.1.4. The mdp parameters are below:
>
> Thank you in advance,
>
> Sincerely,
> Neha
>
>
>
> title= OPLS Lysozyme NPT equilibration
> define= -DPOSRES_CNT; position restrain the protein
> ; Run parameters
> integrator= md; leap-frog integrator
> nsteps= 50; 2
> dt= 0.001; 2 fs
> ; Output control
> nstxout= 5000; save coordinates every 1.0 ps
> nstvout= 5000; save velocities every 1.0 ps
> nstenergy= 5000; save energies every 1.0 ps
> nstlog= 5000; update log file every 1.0 ps
> ;energygrps   = Protein  CNT Water NA
> ; Bond parameters
> continuation= yes; Restarting after NVT
> constraint_algorithm= lincs; holonomic constraints
> constraints= all-bonds; all bonds (even heavy atom-H
> bonds) constrained
> lincs_iter= 1; accuracy of LINCS
> lincs_order= 4; also related to accuracy
> ; Neighborsearching
> cutoff-scheme   = Verlet
> ns_type= grid; search neighboring grid cells
> nstlist= 10; 20 fs, largely irrelevant with Verlet
> scheme
> rcoulomb= 1.0; short-range electrostatic cutoff (in nm)
> rvdw= 1.0; short-range van der Waals cutoff (in nm)
> ; Electrostatics
> coulombtype= PME; Particle Mesh Ewald for long-range
> electrostatics
> pme_order= 4; cubic interpolation
> fourierspacing= 0.16; grid spacing for FFT
> ; Temperature coupling is on
> tcoupl= Berendsen; modified Berendsen
> thermostat
> tc-grps= CNT Water; two coupling groups - more accurate
> tau_t= 0.2  0.2; time constant, in ps
> ref_t= 310   310   ; reference temperature, one for
> each group, in K
> ; Pressure coupling is on
> pcoupl= Berendsen; Pressure coupling on in NPT
> pcoupltype= isotropic; uniform scaling of box
> vectors
> tau_p= 5.0; time constant, in ps
> ref_p= 1.0; reference pressure, in bar
> compressibility = 4.5e-5; isothermal compressibility of
> water, bar^-1
> refcoord_scaling= com
> ; Periodic boundary conditions
> pbc= xyz; 3-D PBC
> periodic_molecules = yes
> ; Dispersion correction
> DispCorr= EnerPres; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel= no; Velocity generation is off
>
> --
> Regards,
> Dr. Neha S. Gandhi,
>
>
> --
>
> Message: 2
> Date: Sun, 8 Oct 2017 22:34:21 +0530
> From: Dilip H N <cy16f01.di...@nitk.edu.in>
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] Regarding charges for atoms in a molecule
> Message-ID:
> <CAD6GXy07bfJ8BMOdi68a6rjkvf-tTF9kWF_VroK9nKfVdDQ-wA@mail.
> gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hello,
> I have an amino-aci

[gmx-users] Equilibration using position restraints in NPT

2017-10-08 Thread Neha Gandhi

This is a very common post on previous mailing list however, I am still not
able to fix the problem of position restraints during NPT.

I have a carbon nanotube aligned to z-direction. I am trying to simulate
infinite nanotube using periodic conditions. It is common to use position
restraints for nanotube (most papers report this). I have imposed position
restraints on nanotube and in doing so, the coordinates fluctuates by 0.5-1
nm. This is not an issue with NVT simulation (Berendsen thermostat and
barostat). I tried different thermostats and barostats, they deform the
nanotube as previously discussed on gromacs mailing list.

How do I equilibrate nanotube system with position restraints when used
together with pressure coupling? Should I play with the box size after
first NVT run?
The force field is opls based on gromacs guideline on CNTs and GROMACS
version is 5.1.4. The mdp parameters are below:

Thank you in advance,

Sincerely,
Neha



title= OPLS Lysozyme NPT equilibration
define= -DPOSRES_CNT; position restrain the protein
; Run parameters
integrator= md; leap-frog integrator
nsteps= 50; 2
dt= 0.001; 2 fs
; Output control
nstxout= 5000; save coordinates every 1.0 ps
nstvout= 5000; save velocities every 1.0 ps
nstenergy= 5000; save energies every 1.0 ps
nstlog= 5000; update log file every 1.0 ps
;energygrps   = Protein  CNT Water NA
; Bond parameters
continuation= yes; Restarting after NVT
constraint_algorithm= lincs; holonomic constraints
constraints= all-bonds; all bonds (even heavy atom-H
bonds) constrained
lincs_iter= 1; accuracy of LINCS
lincs_order= 4; also related to accuracy
; Neighborsearching
cutoff-scheme   = Verlet
ns_type= grid; search neighboring grid cells
nstlist= 10; 20 fs, largely irrelevant with Verlet
scheme
rcoulomb= 1.0; short-range electrostatic cutoff (in nm)
rvdw= 1.0; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype= PME; Particle Mesh Ewald for long-range
electrostatics
pme_order= 4; cubic interpolation
fourierspacing= 0.16; grid spacing for FFT
; Temperature coupling is on
tcoupl= Berendsen; modified Berendsen thermostat
tc-grps= CNT Water; two coupling groups - more accurate
tau_t= 0.2  0.2; time constant, in ps
ref_t= 310   310   ; reference temperature, one for
each group, in K
; Pressure coupling is on
pcoupl= Berendsen; Pressure coupling on in NPT
pcoupltype= isotropic; uniform scaling of box
vectors
tau_p= 5.0; time constant, in ps
ref_p= 1.0; reference pressure, in bar
compressibility = 4.5e-5; isothermal compressibility of
water, bar^-1
refcoord_scaling= com
; Periodic boundary conditions
pbc= xyz; 3-D PBC
periodic_molecules = yes
; Dispersion correction
DispCorr= EnerPres; account for cut-off vdW scheme
; Velocity generation
gen_vel= no; Velocity generation is off

-- 
Regards,
Dr. Neha S. Gandhi,
-- 
Gromacs Users mailing list

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[gmx-users] GROMACS 5.1.0 crashes on pbs queue system

2017-02-15 Thread Neha Gandhi

Dear List,

I have compiled gromacs 5.1.0 using MPI. The job runs interactively as well
as through pbs submission using two nodes. However, the job crashes
immediately when I submit more than two jobs. Below is the error:
--
mpirun noticed that process rank 18 with PID 153374 on node
cl2n045.ib0.hpc.qut.edu.au exited on signal 4 (Illegal instruction).
--
24 total processes killed (some possibly by mpirun during cleanup)

-
PBS Job 1662894.pbs
CPU time  : 00:00:34
Wall time : 00:00:05
Mem usage : 256kb

Any input is much appreciated.

-- 
Regards,
Dr. Neha S. Gandhi,
Vice Chancellor's Research Fellow,
Queensland University of Technology,
2 George Street, Brisbane, QLD 4000
Australia
LinkedIn
Research Gate
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[gmx-users] GROMACS 5.1.2 performance

2016-12-14 Thread Neha Gandhi

Dear list,

I think the question on gromacs performance on cpu cluster has been raised
many times in the mailing list. My apologies for reiterating the question.
I am using a system ~8 atoms with virtual sites (hence timestep of 4
fs). The job hasn't completed yet but it seems that the jobs are running
slower than my experience running with older versions of GROMACS.

Here is the job script
#!/bin/bash -l
#PBS -N sgk
#PBS -l walltime=24:00:00
#PBS -l select=6:ncpus=16:mpiprocs=16:mem=20gb
#PBS -j oe

export OMP_NUM_THREADS=1

module purge
module load gromacs/5.1.2-foss-2016a-hybrid
mpirun -np 96 gmx_mpi mdrun -v -deffnm npt


and the output log indicates load imbalance :

Number of logical cores detected (48) does not match the number reported by
OpenMP (10).
Consider setting the launch configuration manually!

Running on 6 nodes with total 248 logical cores
  Logical cores per node:   40 - 48
Hardware detected on host cl3n073 (the node of MPI rank 0):
  CPU info:
Vendor: GenuineIntel
Brand:  Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz
Family:  6  model: 63  stepping:  2
CPU features: apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt lahf_lm
mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sse2
sse3 sse4.1 sse4.2 ssse3 tdt x2apic
SIMD instructions most likely to fit this hardware: AVX_256 - AVX2_256
SIMD instructions selected at GROMACS compile time: AVX_256


DD  step 34999  vol min/aver 0.553  load imb.: force 46.2%  pme mesh/force
0.506

   Step   Time Lambda
  35000   70.00.0

   Energies (kJ/mol)
   G96AngleProper Dih.  Improper Dih.  LJ-14 Coulomb-14
9.21820e+036.85434e+032.03852e+03   -4.52887e+018.24856e+04
LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.  Potential
1.76075e+05   -4.85764e+03   -1.52098e+063.15077e+03   -1.24606e+06
Kinetic En.   Total EnergyTemperature Pres. DC (bar) Pressure (bar)
2.19009e+05   -1.02705e+062.99843e+02   -8.61175e+01   -1.48459e+02
   Constr. rmsd
2.75565e-05

DD  step 3  vol min/aver 0.475  load imb.: force 89.0%  pme mesh/force
0.948

   Step   Time Lambda
  4   80.00.0

   Energies (kJ/mol)
   G96AngleProper Dih.  Improper Dih.  LJ-14 Coulomb-14
9.32970e+036.83305e+032.07167e+03   -2.67360e+018.24534e+04
LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.  Potential
1.78434e+05   -4.86516e+03   -1.52332e+063.15600e+03   -1.24593e+06
Kinetic En.   Total EnergyTemperature Pres. DC (bar) Pressure (bar)
2.19647e+05   -1.02628e+063.00717e+02   -8.63844e+017.45115e+01
   Constr. rmsd
2.80701e-05

DD  step 44999  vol min/aver 0.704  load imb.: force 106.3%  pme mesh/force
0.720

   Step   Time Lambda
  45000   90.00.0

   Energies (kJ/mol)
   G96AngleProper Dih.  Improper Dih.  LJ-14 Coulomb-14
9.30472e+036.53990e+032.08250e+031.40282e+018.27162e+04
LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.  Potential
1.77677e+05   -4.87223e+03   -1.52383e+063.05237e+03   -1.24731e+06
Kinetic En.   Total EnergyTemperature Pres. DC (bar) Pressure (bar)
2.19610e+05   -1.02770e+063.00666e+02   -8.66354e+014.81709e+01
   Constr. rmsd
2.77685e-05

Writing checkpoint, step 46075 at Wed Dec 14 21:28:11 2016


DD  step 4  vol min/aver 0.543  load imb.: force 16.6%  pme mesh/force
0.848

   Step   Time Lambda
  5  100.00.0

   Energies (kJ/mol)
   G96AngleProper Dih.  Improper Dih.  LJ-14 Coulomb-14
9.09212e+036.76222e+031.95816e+03   -6.36247e+018.23450e+04
LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.  Potential
1.77732e+05   -4.87147e+03   -1.52371e+063.15838e+03   -1.24760e+06
Kinetic En.   Total EnergyTemperature Pres. DC (bar) Pressure (bar)
2.18646e+05   -1.02895e+062.99346e+02   -8.66085e+011.49550e+01
   Constr. rmsd
2.95505e-05

I appreciate your feedback.

Regards,
Neha
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[gmx-users] extending simulation

2016-08-10 Thread Neha Gandhi

Dear List,

I have only .xtc, .edr, .top and .tpr files. I want to extend my runs. I
tried converting .xtc to .trr. Then I tried using both grompp and/or
convert-tpr tools to extend my runs as recommended by gromacs manual.

However, when I input new tpr file to mdrun it starts the run with time=0
ps. I want the simulation to start with t=50 ns after previous run.

Is there a way to work around this without .cpt file?

Regards,
Neha
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[gmx-users] gromacs on multiple gpus

2016-05-09 Thread Neha Gandhi

Dear List,

I have compiled GROMACS 5.0.7 using following options

CMAKE_PREFIX_PATH=/home/gandhin/fftw cmake .. -DGMX_BUILD_OWN_FFTW=OFF
-DGMX_MPI=on -DGMX_GPU=on -DGMX_SIMD=AVX2_256
-DCMAKE_C_COMPILER=${MPICCDIR}mpicc -DCMAKE_CXX_COMPILER=${MPICCDIR}mpicxx
-DGMX_BUILD_MDRUN_ONLY=on -DCMAKE_INSTALL_PREFIX=/home/gandhin/gromacs-5.0.7

The machine has two K40 gpus and 12 cpus per node. When I submit jobs using
mpirun gmx_mpi mdrun -v.. the program mdrun detects two gpus with ids #0
and #1 but it still runs the job with only one gpu i.e. gpu id #0. What is
the correct way of submitting job (using PBS) so that both gpus and 12
cores on the same node are utilised by mdrun for the simulation?

My apologies to post this question to GROMACS mailing list, this post is
more related to the system admin who aren't able to help.

Thank you for kind attention

Regards,
Neha





-- 
Regards,
Dr. Neha S. Gandhi,
Vice Chancellor's Research Fellow,
Queensland University of Technology,
2 George Street, Brisbane, QLD 4000
Australia
LinkedIn
Research Gate
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Re: [gmx-users] Carbohydrate GAG simulations

2015-09-03 Thread Neha Gandhi

Hi Lara,

I have worked extensively on GAGS in particular heparin. You may wish to
refer to my publications.

Glycam has residues for sulphated glucuronic acid/iduronic acid as well as
sulphated glucosamine. You can build topologies for heparin using glycam
webserver. If you wish to run your simulation in GROMACS, you can convert
glycam amber topologies to gromacs format using Acpype.

There are no direct parameters in GROMOS force fields to build sulfated
GAGs (although parameters exist for hexapyranoses). Hugo Verli has used
GROMOS force fields to simulate heparin oligosaccharide. Kindly refer to
his publications for parameters for GAGs.

CHARMM has parameters for GAGs like CS, DS but they lack parameters for
N-sulfated glucosamine. You can use Charmm-gui to obtain parameters.

I hope this helps,

Best,
Neha

On 4 September 2015 at 08:54, Lara rajam  wrote:

> Dear Users !
> I would like to do a GAG ( heparin simulation ) with gromacs. can any one
> tell me the appropriate links related to this
> that will be useful for a beginner like me
>
> thank you !
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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> posting!
>
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> send a mail to gmx-users-requ...@gromacs.org.
>

-- 
Regards,
Dr. Neha S. Gandhi,
Curtin Research Fellow,
School of Biomedical Sciences,
Curtin University,
Perth GPO U1987
Australia
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[gmx-users] REMD exchange probabilities

2015-03-08 Thread Neha Gandhi

Dear list,

Using an exchange probability of 0.25 and temperature range 293-370  K, I
calculated number of replicas using the server. However, when I did first
run and tried exchanging replicas every 500 steps (1 ps), I don't think the
exchange probabilities make sense in particular replicas 15 and 16. Replica
15 has a low exchange ratio of 0.12 while replica 16 has a high exchange
ratio of 0.55.

Repl  average probabilities:
Repl 0123456789   10   11   12
13   14   15   16   17   18   19   20   21   22   23   24   25   26   27
28   29   30   31   32   33   34   35   36   37   38   39   40   41   42
43   44   45   46   47
Repl  .28  .28  .28  .28  .29  .28  .29  .29  .28  .29  .28  .28  .29
.29  .29  .12  .55  .29  .29  .30  .30  .29  .29  .26  .32  .31  .30  .30
.30  .30  .30  .31  .31  .31  .31  .31  .31  .31  .31  .31  .31  .31  .32
.32  .32  .32  .33
Repl  number of exchanges:
Repl 0123456789   10   11   12
13   14   15   16   17   18   19   20   21   22   23   24   25   26   27
28   29   30   31   32   33   34   35   36   37   38   39   40   41   42
43   44   45   46   47
Repl 2901 2954 2873 3017 3038 2910 3009 2993 2934 3002 2981 2999 2927
3038 3059 1229 5757 3056 3100 3136 3054 3053 3109 2743  3166 3097 3185
3161 3189 3133 3226 3261 3242 3229 3205 3249 3227 3221 3222 3326 3303 3309
3320 3373 3346 3474
Repl  average number of exchanges:
Repl 0123456789   10   11   12
13   14   15   16   17   18   19   20   21   22   23   24   25   26   27
28   29   30   31   32   33   34   35   36   37   38   39   40   41   42
43   44   45   46   47
Repl  .28  .28  .27  .29  .29  .28  .29  .29  .28  .29  .29  .29  .28
.29  .29  .12  .55  .29  .30  .30  .29  .29  .30  .26  .32  .30  .30  .30
.30  .31  .30  .31  .31  .31  .31  .31  .31  .31  .31  .31  .32  .32  .32
.32  .32  .32  .33


Below are the temperatures I have used. How do I manually edit temperatures
to get average exchange probabilities between 0.2-0.3?

ref_t= 293293; reference temperature, one for each
group, in K
ref_t= 294.51 294.51; reference temperature, one for each
group, in K
ref_t= 296.03 296.03; reference temperature, one for each
group, in K
ref_t= 297.56 297.56; reference temperature, one for each
group, in K
ref_t= 299.09 299.09; reference temperature, one for each
group, in K
ref_t= 300.63 300.63; reference temperature, one for each
group, in K
ref_t= 302.18 302.18; reference temperature, one for each
group, in K
ref_t= 303.73 303.73; reference temperature, one for each
group, in K
ref_t= 305.29 305.29; reference temperature, one for each
group, in K
ref_t= 306.86 306.86; reference temperature, one for each
group, in K
ref_t= 308.43 308.43; reference temperature, one for each
group, in K
ref_t= 310.01 310.01; reference temperature, one for each
group, in K
ref_t= 311.60 311.60; reference temperature, one for each
group, in K
ref_t= 313.19 313.19; reference temperature, one for each
group, in K
ref_t= 314.79 314.79; reference temperature, one for each
group, in K
ref_t= 316.40 316.40; reference temperature, one for each
group, in K
ref_t= 318.63 318.63; reference temperature, one for each
group, in K
ref_t= 319.63 319.63; reference temperature, one for each
group, in K
ref_t= 321.26 321.26; reference temperature, one for each
group, in K
ref_t= 322.89 322.89; reference temperature, one for each
group, in K
ref_t= 324.52 324.52; reference temperature, one for each
group, in K
ref_t= 326.17 326.17; reference temperature, one for each
group, in K
ref_t= 327.82 327.82; reference temperature, one for each
group, in K
ref_t= 329.49 329.49; reference temperature, one for each
group, in K
ref_t= 331.26 331.26; reference temperature, one for each
group, in K
ref_t= 332.86 332.86; reference temperature, one for each
group, in K
ref_t= 334.51 334.51; reference temperature, one for each
group, in K
ref_t= 336.20 336.20; reference temperature, one for each
group, in K
ref_t= 337.90 337.90; reference temperature, one for each
group, in K
ref_t= 339.61 339.61; reference temperature, one for each
group, in K
ref_t= 341.32 341.32; reference temperature, one for each
group, in K
ref_t= 343.04 343.04; reference temperature, one for each
group, in K
ref_t= 344.76 344.76; reference temperature, one for each
group, in K
ref_t= 346.49 346.49; reference temperature, one for each
group, in K

[gmx-users] centering molecule for movies

2014-07-07 Thread Neha Gandhi

Hi List,

I have simulated peptides in explicit water to form aggregate. I tried
various options to post-process my trajectory (after removing water) using
Gromacs 4.6.3 as described below. I want to record movie using VMD but the
molecule translates and rotates during movie hence, I cannot capture all
screen shots properly.

trjconv -f md.xtc -pbc mol -o x.xtc -s md.tpr -n index.ndx
trjconv -f x.xtc -ur compact -center -s md.tpr -n index.ndx

How do I keep the peptides in center to record the movie? Is it a vmd
problem or post-processing issue will fix it? If anybody has faced similar
issue and has found a solution, i would appreciate your help.

Many thanks,
Neha
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[gmx-users] Martini in Gromacs

2014-06-10 Thread Neha Gandhi

Hello,

I am trying to run coarse grained MD in gromacs. I get following errors,
should I reduce the time step? Your feedback is appreciated.


NOTE 1 [file prod1.mdp]:
  nstcomm  nstcalcenergy defeats the purpose of nstcalcenergy, setting
  nstcomm to nstcalcenergy


NOTE 2 [file prod1.mdp]:
  The Berendsen thermostat does not generate the correct kinetic energy
  distribution. You might want to consider using the V-rescale thermostat.


WARNING 1 [file prod1.mdp]:
  For proper integration of the Parrinello-Rahman barostat, tau-p (2)
  should be at least 20 times larger than nstpcouple*dt (0.2)


NOTE 3 [file prod1.mdp]:
  The switch/shift interaction settings are just for compatibility; you
  will get better performance from applying potential modifiers to your
  interactions!


Generated 0 of the 780 non-bonded parameter combinations
Excluding 1 bonded neighbours molecule type 'Protein_A'
Excluding 1 bonded neighbours molecule type 'W'
Excluding 1 bonded neighbours molecule type 'CL-'

WARNING 2 [file topol.top, line 16]:
  The bond in molecule-type Protein_A between atoms 1 BB and 3 BB has an
  estimated oscillational period of 9.7e-02 ps, which is less than 5 times
  the time step of 2.0e-02 ps.
  Maybe you forgot to change the constraints mdp option.


WARNING 3 [file prod1.mdp]:
  For proper integration of the Berendsen thermostat, tau-t (0.5) should be
  at least 5 times larger than nsttcouple*dt (0.2)

Number of degrees of freedom in T-Coupling group Protein is 11517.00
Number of degrees of freedom in T-Coupling group Other is 198744.00
Reading Coordinates, Velocities and Box size from old trajectory
Will read whole trajectory
Last frame -1 time 5.000
Using frame at t = 5 ps
Starting time for run is 0 ps

NOTE 4 [file prod1.mdp]:
  This run will generate roughly 48891 Mb of data


There were 4 notes

There were 3 warnings

---
Program grompp, VERSION 4.6.3
Source code file: /ivec/build/gromacs-4.6.3/src/kernel/grompp.c, line: 1910

Fatal error:
Too many warnings (3), grompp terminated.
If you are sure all warnings are harmless, use the -maxwarn option.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

Here is the mdp file
; RUN CONTROL PARAMETERS =
integrator   = md
; start time and timestep in ps =
tinit= 0.0
dt   = 0.020
nsteps = 12500
; 125 mio steps x 20fs = 2500ns = 10* microsec
; number of steps for center of mass motion removal
nstcomm  = 1
; group(s) for center of mass motion removal
comm-grps= Protein Other

; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout  = 5000
nstvout  = 5000
nstfout  = 0
; Output frequency for energies to log file and energy file =
nstlog   = 5000
nstenergy= 5000
; Output frequency and precision for xtc file =
nstxtcout= 5000
xtc_precision= 100
; This selects the subset of atoms for the xtc file. You can =
; select multiple groups. By default all atoms will be written. =
xtc-grps = System
; Selection of energy groups =
energygrps   = Protein Other

; NEIGHBORSEARCHING PARAMETERS =
; nblist update frequency =
nstlist  = 10
; ns algorithm (simple or grid) =
ns_type  = grid
; Periodic boundary conditions: xyz or none =
pbc  = xyz
; nblist cut-off =
rlist= 1.4

; OPTIONS FOR ELECTROSTATICS AND VDW =
; Method for doing electrostatics =
coulombtype  = Shift
rcoulomb_switch  = 0.0
rcoulomb = 1.2
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon_r= 15
; Method for doing Van der Waals =
vdw_type = Shift
; cut-off lengths=
rvdw_switch  = 0.9
rvdw = 1.2
; Apply long range dispersion corrections for Energy and Pressure =
DispCorr = No

; OPTIONS FOR WEAK COUPLING ALGORITHMS =
; Temperature coupling   =
tcoupl   = Berendsen
; Groups to couple separately =
tc-grps  = Protein Other
; Time constant (ps) and reference temperature (K) =
tau_t= 0.5  0.5
ref_t= 310 310
; Pressure coupling  =
Pcoupl   = Parrinello-Rahman
Pcoupltype   = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p= 2.00
compressibility  = 5e-5
ref_p= 1.0

; GENERATE VELOCITIES FOR STARTUP RUN =
gen_vel  = no
gen_temp = 310
gen_seed = 473529

; OPTIONS FOR BONDS =

[gmx-users] g_cluster

2014-06-09 Thread Neha Gandhi

Hi List,

I have come across mailing list where g_cluster can possibly be used for
clustering of docked ligands. I tried g_cluster but it will change the
reference coordinates with respect to the receptor.

Is there a way to do clustering using g_cluster based on binding site?

Many thanks,
Neha

-- 
Regards,
Dr. Neha S. Gandhi,
Curtin Research Fellow,
School of Biomedical Sciences,
Curtin University,
Perth GPO U1987
Australia
LinkedIn
Research Gate
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[gmx-users] counter ions in coarse grained simulations

2014-05-22 Thread Neha Gandhi

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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[gmx-users] gromacs bond restraints

2014-01-15 Thread Neha Gandhi

How can I impose restraints in gromacs .mdp file or topology file to
avoid isomerization of the peptide bond at the highest temperatures?

Your help is appreciated

-- 
Regards,
Dr. Neha S. Gandhi,
Curtin Research Fellow,
School of Biomedical Sciences,
Curtin University,
Perth GPO U1987
Australia
LinkedIn
Research Gate
-- 
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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[gmx-users] multiple nodes

[gmx-users] Equilibration using position restraints in NPT

[gmx-users] Equilibration using position restraints in NPT

[gmx-users] GROMACS 5.1.0 crashes on pbs queue system

[gmx-users] GROMACS 5.1.2 performance

[gmx-users] extending simulation

[gmx-users] gromacs on multiple gpus

Re: [gmx-users] Carbohydrate GAG simulations

[gmx-users] REMD exchange probabilities

[gmx-users] centering molecule for movies

[gmx-users] Martini in Gromacs

[gmx-users] g_cluster

[gmx-users] counter ions in coarse grained simulations

[gmx-users] gromacs bond restraints

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