[gmx-users] Suggestion required for calculation of membrane contact sites and Lipid binding strength

2016-05-28 Thread Antara mazumdar
Dear Gromacs users,

Can anyone suggest me a way to find the membrane contact sites i.e. the
lipids that are making contact with protein residues with respect to time
from a  membrane protein simulation? I have calculated the distance and
contact of protein residues from upper leaflet atoms of bilayer already
with a cutoff between 0.5 nm and 0.7 nm.

I have the lipid numbers in the log file from g_hbond as well as g_dist.
Should i be taking all these into account or a cutoff needs to be taken and
can this be calculated wrt time?

Secondly, has anyone found out the lipid binding strength from membrane
protein simulations? Can we call the frequency of a protein residue to make
a contact as its lipid binding strength? Here also, is there some way to
find the binding strength wrt time?

Thanks!!
Kind Regards,
Antara

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[gmx-users] Re : mdrun errors with gromacs 5.1 in parallel

2016-05-26 Thread Antara mazumdar
Dear Mark,

Thanks for the suggestion. I will tell them that.
Kind Regards,
Antara

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[gmx-users] Re : mdrun errors with gromacs 5.1 in parallel

2016-05-26 Thread Antara mazumdar
Dear Mark,

   I will ask our HPC support team to check the MPI enabled version of
gromacs then. Thank you for your suggestion.
Kind Regards,
Antara

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[gmx-users] Re : mdrun errors with gromacs 5.1 in parallel

2016-05-26 Thread Antara mazumdar
Dear Users,
  I was trying to do equilibration of a mixed lipid vesicle using gromacs
5.1 in parallel using the below pasted pbs script :


#!/bin/tcsh
#PBS -l walltime=48:00:00
#PBS -N VES_new_16
#PBS -q workq
#PBS -l select=1:ncpus=16:mpiprocs=16
#PBS -V

# Go to the directory from which you submitted the job
cd $PBS_O_WORKDIR

#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
#export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/home1/gkpatra/gmp/lib
module load intel-cluster-studio-2013


setenv OMP_NUM_THREADS 1
/home/lipi/openmpi164/bin/mpirun -np 16
/app/setups/gromacs-5.1.1/build/bin/gmx mdrun mpi -deffnm
step6.2_equilibration -rdd 1.8 > test.dat

This is generating multiple output and checkpoint files while its trying to
run :


 #step6.2_equilibration.xtc.6#
 #step6.2_equilibration_step4400.cpt.1#
 #step6.2_equilibration.log.3#
#step6.2_equilibration.log.5#
 #step6.2_equilibration.log.4#
 #step6.2_equilibration.log.2#
 step6.2_equilibration_prev.cpt
 #step6.2_equilibration.log.6#
step6.2_equilibration.cpt
#step6.2_equilibration.xtc.3#
 #step6.2_equilibration.xtc.5#
#step6.2_equilibration.xtc.7#
step6.2_equilibration.xtc

When i check the log file to see the errors , it is showing the following :

  Step   Time Lambda
  00.00.0

   Energies (kJ/mol)
   Bond   G96AngleLJ (SR)   Coulomb (SR)   Coul. recip.
1.18159e+053.78079e+04   -8.79894e+06   -1.10782e+064.70754e+05
Flat-bottom posres  PotentialKinetic En.   Total Energy
Temperature
4.65013e+06   -4.62990e+062.25820e+02   -4.62968e+066.73923e-02
 Pressure (bar)
   -7.74545e+01

DD  step 39 load imb.: force 22.2%

Writing checkpoint, step 560 at Thu May 26 11:57:56 2016



---
Program gmx mdrun, VERSION 5.1.1
Source code file:
/app/setups/gromacs-5.1.1/src/gromacs/gmxlib/checkpoint.cpp, line: 1670

File input/output error:
Cannot rename checkpoint file; maybe you are out of disk space?
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors



I am not able to find the solution for it. What could be causing this? I
have not been able to find help from HPC support available to us.



Kind Regards,
Antara

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[gmx-users] mdrun terminated with errors with gromacs 5.1 in parallel

2016-05-25 Thread Antara mazumdar
Dear Gromacs users,

   I was trying to do equilibration of a mixed lipid vesicle using gromacs
5.1 in parallel.
My pbs script file details for this is the following :

/home/lipi/openmpi164/bin/mpirun -np 48
/app/setups/gromacs-5.1.1/build/bin/gmx mdrun mpi -deffnm
step6.2_equilibration -rdd 1.8 > test.dat


However, the mdrun is terminated with the following two errors.

*1)Cannot rename checkpoint file; maybe you are out of disk space?*

i have checked the disk space, it still has terabytes of space left to be
used. The folder where i am running it is hardly 45 MB.


*2)mpirun noticed that process rank 10 with PID 62690 on node cn0013 exited
on signal 11 (Segmentation fault).*
Can anyone suggest me how to resolve it?


Kind Regards,
Antara

--
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[gmx-users] help required in calculation of domain decomposition for a mixed lipid vesicle system

2016-05-24 Thread Antara mazumdar
Dear gromacs users,


I am trying to calculate domain decomposition of a mixed lipid vesicle
system OF SIZE 268675 Atoms and box size is 32 X 32 X 32 nm to be able to
run in parallel.

I want to calculate the number of PME nodes per total number of nodes.
However, i am not clear on how to calculate the value of nPME here. I would
also mention that number of nodes that can be used need to be multiple of
16 and the value of minimum cell size is 1.8 nm.

Can someone guide me in this regard?
Kind Regards,
Antara

--
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[gmx-users] Re : WARNING no output error while dumping structures with trjconv from MD.trr

2016-05-23 Thread Antara mazumdar
Dear Mark,

   I checked the file size , MD.trr is 3.2 Terabytes. It is a million atom
system. What further could be done?
Kind Regards,
Antara

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[gmx-users] Re : WARNING no output error while dumping structures with trjconv from MD.trr

2016-05-21 Thread Antara mazumdar
Dear Sir,

The MD.trr i expect to be having 382ns of data as is mentioned in the log
file and MD.xtc that was generated alongwith MD.trr when the simulation
ran  has 382ns.

However, MD.trr has problems in giving output beyond 25ns. Could it be
corruption of frames or something?
Kind Regards,
Antara

--
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[gmx-users] help required in plotting percentage of protein in contact with membrane vs time

2016-05-21 Thread Antara mazumdar
Dear Gromacs users,

  I have a membrane protein simulation performed with gromacs 4.6. I have
calculated the minimum distance of protein residues from upper leaflet of
the lipid bilayer. I also have the time wise atom pair contacts as an
output.
The following command i used :

g_mindist -f SYSTEM_FIT_SIM4_DT100.xtc -s MD_4_NOWATER.tpr -n ../index.ndx
-d 0.7 -o atompair -on numcontact -od mindist.xvg

The atom pair out output i got was as follow :

.00e+00  2412281928
1.00e+02  1630266151
2.00e+02  1630266151
3.00e+02  2410284225
4.00e+02  2412284225
5.00e+02  2412284225
6.00e+02  2410284225
7.00e+02  2410284225
8.00e+02  2410284225
9.00e+02  2410284225
1.00e+03  2405284225
1.10e+03  2411281928
1.20e+03  2412284225
1.30e+03  2332285163
1.40e+03  2411284225
1.50e+03  2410284225
1.60e+03  1555264261
1.70e+03  1555264261
1.80e+03  1555264261
1.90e+03  1554266958
2.00e+03  2389266958
2.10e+03  2411285163
2.20e+03  2412285163
2.30e+03  2412285163
2.40e+03  2410285163
2.50e+03  2410285163
2.60e+03  2412285163


 I now need to find out time wise percentage of protein covering the
membrane. I want to know for instance, at time t=0ns, what is the protein
coverage % and similarly for the entire trajectory i want to calculate this.


Kindly suggest something!!

Kind Regards,
Antara

--
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Systems biology group
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M : +91-9717970040
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[gmx-users] WARNING no output error while dumping structures with trjconv from MD.trr

2016-05-21 Thread Antara mazumdar
Dear gromacs users,

   I was trying to dump structures from MD.trr using trjconv. The MD.trr
has 0ns to 382ns of data. (i checked the MD.log file also).  However, when
i try to dump structures beyond 25ns, with the following command :
*gmx trjconv mpi -f MD.trr -dump 27000.000 -dt 1000 -s MD.tpr -b 2.000*


*it gives the following error :WARNING no output, last frame read at
t=25290*

I have also tried to check with gmxcheck but it only runs till 20ns.

trjconv and or gmxcheck did not give any error with MD.xtc which was
generated during the simulation.

I require the MD.trr as i  need velocity and force information for my
analysis.

Kindly suggest something!!
Kind Regards,
Antara

--
Junior research fellow(project)
Systems biology group
CSIR-Institute of Genomics & Integrative Biology
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M : +91-9717970040
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[gmx-users] help required in calculating npme value for domain decomposition

2016-05-19 Thread Antara mazumdar
Dear gromacs users,

  I need help in calculating the value of npme for the purpose of domain
decomposition for my system of mixed lipid vesicles.


Thanks!!
Kind Regards,
Antara

--
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Re: [gmx-users] Help required for calculation of protein coverage % wrt time

2016-05-19 Thread Antara mazumdar
Dear users,

Is there any script available to calculate % occupancy of residues with
respect to time? This in continuation with my previous query on percentage
of protein in contact with membrane??

Kind Regards,
Antara

--
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Systems biology group
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M : +91-9717970040
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On Thu, May 19, 2016 at 6:35 PM, Antara mazumdar <antara.mazum...@igib.in>
wrote:

> Dear gromacs users,
>
> I have a peripheral membrane protein which I have simulated using Charmm
> 36 in a mixed lipids bilayer. I want to calculate the percentage of protein
> in contact with membrane wrt time. I already have residue wise distances
> from membrane calculated.
>
> Can anyone suggest me how to go about it after this?
>
> Antara Mazumdar
>
> ISCB SC RSG-India
>
> Core Committee Member
>
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[gmx-users] Help required for calculation of protein coverage % wrt time

2016-05-19 Thread Antara mazumdar
Dear gromacs users,

I have a peripheral membrane protein which I have simulated using Charmm 36
in a mixed lipids bilayer. I want to calculate the percentage of protein in
contact with membrane wrt time. I already have residue wise distances from
membrane calculated.

Can anyone suggest me how to go about it after this?

Antara Mazumdar

ISCB SC RSG-India

Core Committee Member
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Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 145, Issue 55

2016-05-15 Thread Antara mazumdar
; What happens when you run on one rank?
> >
> >> For the production tpr, i used the gro file from the last equilibration
> > step(step6.6) The command used was :
> >>
> >> gmx grompp -c step6.6equilibration.gro -p system.top -n new_index.ndx -f
> > MD.mdp -o MD.tpr
> >
> > That looks like it could be reasonable, but as with any equilibration you
> > need to look at observables to judge that it's equilibrated. Their
> builder
> > should provide reasonable defaults, but you can't assume they're perfect,
> > either. In particular, if the last equilibration ensemble doesn't match
> the
> > production ensemble, that could be the problem.
> >
>
> Failing to pass the .cpt file to grompp -t after equilibration is a great
> way to
> do that.  The production simulation is starting from some unpredictable
> ensemble, without velocities, etc..
>
> -Justin
>
> > Mark
> >
> > On Sat, May 14, 2016 at 5:10 PM Mark Abraham <mark.j.abra...@gmail.com>
> > wrote:
> >
> >> Hi,
> >>
> >> On Sat, May 14, 2016 at 4:34 PM Antara mazumdar <
> antara.mazum...@igib.in>
> >> wrote:
> >>
> >>> Dear users,
> >>>
> >>> I am trying to run a coarse grained simulation of a membrane protein
> in a
> >>> mixed lipid billayer using martini model 2.2. I have already performed
> all
> >>> the equilibration steps successfully on my desktop with GROMACS 5.1.0.
> >>> However, when i try to execute its production run in parallel(having
> >>> gromacs 5.1 version installed)  it complains of LINCS warning and
> >>> terminates at step 0. The lincs warning error is coming from BB and SC1
> >>> atoms of one of the protein residues.
> >>>
> >>
> >> There are lots of possible places to go wrong, including not making your
> >> production .tpr based on the outputs of your equilibration. This seems
> >> quite a likely possibility.
> >>
> >> You should also consider further equilibration - whether using Martini
> or
> >> not, it is sometimes necessary to use a small time step when relaxing
> >> problem configurations.
> >>
> >>
> >>>  But on the contrary, it runs on the desktop successfully. *My
> production
> >>> run mdp file details are below :*
> >>>
> >>>
> >>> .
> >>>
> >>> This is the MD.mdp file :ntegrator   = md
> >>> tinit= 0.0
> >>> dt   = 0.020
> >>> nsteps   = 25
> >>>
> >>> nstxout  = 2000
> >>> nstvout  = 2000
> >>> nstfout  = 2000
> >>> nstlog   = 2000
> >>> nstenergy= 2000
> >>> nstxtcout= 2000
> >>> xtc_precision= 100
> >>>
> >>> ns_type  = grid
> >>> pbc  = xyz
> >>> nstlist = 10
> >>> cutoff-scheme   = Verlet
> >>> rlist   = 1.2
> >>> vdwtype = Cut-off
> >>> vdw-modifier= none
> >>> rvdw_switch = 1.0
> >>> rvdw= 1.2
> >>> coulombtype = pme
> >>> rcoulomb= 1.2
> >>>
> >>> tcoupl   = v-rescale
> >>> tc-grps  = protein CHOL_POPC_DPSM_DPCE W_ION
> >>>
> >>> tau_t= 1.0 1.0  1.0
> >>> ref_t= 303.15 303.15 303.15
> >>>
> >>> ; Pressure coupling:
> >>> Pcoupl   = berendsen
> >>> Pcoupltype   = semiisotropic
> >>> tau_p= 5.0  5.0
> >>> compressibility  = 3e-4 3e-4
> >>> ref_p= 1.0  1.0
> >>> ; GENERATE VELOCITIES FOR STARTUP RUN:
> >>> gen_vel  = no
> >>> refcoord_scaling = all
> >>>
> >>> *the command used for mdrun :*
> >>>
> >>> -deffnm MD -pin on -rdd 1.8 -np 16
> >>>
> >>
> >> mdrun 5.1 won't accept -np, so I don't know what you are actually doing.
> >> Please don't edit and filture things, copy and paste whole actual
> things.
> >> :-)
> >>
> >> Mark
> 

[gmx-users] error in running mdrun of membrane protein in a mixed bilayer with MARTINI MODEL

2016-05-14 Thread Antara mazumdar
Dear users,

I am trying to run a coarse grained simulation of a membrane protein in a
mixed lipid billayer using martini model 2.2. I have already performed all
the equilibration steps successfully on my desktop with GROMACS 5.1.0.
However, when i try to execute its production run in parallel(having
gromacs 5.1 version installed)  it complains of LINCS warning and
terminates at step 0. The lincs warning error is coming from BB and SC1
atoms of one of the protein residues.

 But on the contrary, it runs on the desktop successfully. *My production
run mdp file details are below :*


.

This is the MD.mdp file :ntegrator   = md
tinit= 0.0
dt   = 0.020
nsteps   = 25

nstxout  = 2000
nstvout  = 2000
nstfout  = 2000
nstlog   = 2000
nstenergy= 2000
nstxtcout= 2000
xtc_precision= 100

ns_type  = grid
pbc  = xyz
nstlist = 10
cutoff-scheme   = Verlet
rlist   = 1.2
vdwtype = Cut-off
vdw-modifier= none
rvdw_switch = 1.0
rvdw= 1.2
coulombtype = pme
rcoulomb= 1.2

tcoupl   = v-rescale
tc-grps  = protein CHOL_POPC_DPSM_DPCE W_ION

tau_t= 1.0 1.0  1.0
ref_t= 303.15 303.15 303.15

; Pressure coupling:
Pcoupl   = berendsen
Pcoupltype   = semiisotropic
tau_p= 5.0  5.0
compressibility  = 3e-4 3e-4
ref_p= 1.0  1.0
; GENERATE VELOCITIES FOR STARTUP RUN:
gen_vel  = no
refcoord_scaling = all

*the command used for mdrun :*

-deffnm MD -pin on -rdd 1.8 -np 16

I would also like to mention that i generated the initial structure of the
system using CHARMM GUI MARTINI MAKER protein-membrane system option. I
have followed the exact builder protocol for the equilibration and
minimisation.

Kindly suggest something!

Thanks,
Antara

--
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Re: [gmx-users] LINCS WARNING Error in running production run in parallel of a MARTINI SYSTEM of membrane protein

2016-05-13 Thread Antara mazumdar
Dear users,

I am trying to run a coarse grained simulation of a membrane protein in a
mixed lipid billayer using martini model 2.2. I have already performed all
the equilibration steps successfully on my desktop with GROMACS 5.1.0.
However, when i try to execute its production run in parallel(having
gromacs 5.1 version installed)  it complains of LINCS warning and
terminates at step 0. But on the contrary, it runs on the desktop
successfully. Kindly suggest something and please let me know if any more
information is required from my side.


Thanks!!

Kind Regards,
Antara

--
Junior research fellow(project)
Systems biology group
CSIR-Institute of Genomics & Integrative Biology
South Campus
New Delhi -  110020
M : +91-9717970040
--



On Fri, May 13, 2016 at 11:11 PM, Antara mazumdar <antara.mazum...@igib.in>
wrote:

> Dear gromacs users,
>
> I am trying to run a coarse grained simulation of a membrane protein in a
> mixed lipid billayer using martini model. I have already performed all the
> equilibration steps successfully on my desktop. However, when i try to
> execute its production run in parallel it complains of LINCS warning and
> terminates at step 0. But on the contrary, it runs on the desktop
> successfully. Kindly suggest something and please let me know if any more
> information is required from my side.
>
>
> Thanks!!
>
>
>
> Kind Regards,
> Antara
>
> --
> Junior research fellow(project)
> Systems biology group
> CSIR-Institute of Genomics & Integrative Biology
> South Campus
> New Delhi -  110020
> M : +91-9717970040
> --
>
>
>
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[gmx-users] LINCS WARNING Error in running production run in parallel of a MARTINI SYSTEM of membrane protein

2016-05-13 Thread Antara mazumdar
Dear gromacs users,

I am trying to run a coarse grained simulation of a membrane protein in a
mixed lipid billayer using martini model. I have already performed all the
equilibration steps successfully on my desktop. However, when i try to
execute its production run in parallel it complains of LINCS warning and
terminates at step 0. But on the contrary, it runs on the desktop
successfully. Kindly suggest something and please let me know if any more
information is required from my side.


Thanks!!



Kind Regards,
Antara

--
Junior research fellow(project)
Systems biology group
CSIR-Institute of Genomics & Integrative Biology
South Campus
New Delhi -  110020
M : +91-9717970040
--
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[gmx-users] URGENT query regarding pbc = no in grompp in membrane simulations

2015-06-03 Thread Antara mazumdar
i want to simulate a system having membrane and proteins with pbc=no to
allow surface effects. I use the following settings in my production mdp
file :

 Run parameters
integrator  = md; leap-frog integrator
nsteps  = 1 ; 2 * 1 = 2 ms
dt  = 0.002 ; 2 fs
; Output control
;trr file
nstxout = 50; save coordinates every 1ns
nstvout = 50; save velocities every 1ns
nstenergy   = 1 ; save energies every 20ps
nstlog  = 1 ; update log file every 20ps
;xtc file
nstxtcout   = 1 ; xtc compressed trajectory output every 20
ps
; Bond parameters
constraint_algorithm   = LINCS; holonomic constraints
constraints=   none


;ns-type= simple
nstlist = 0
rlist   = 0
coulombtype = Cut-off
rcoulomb= 0.0
rvdw= 0

Periodic boundary conditions
pbc = no; 3-D PBC
; Velocity generation
gen_vel = YES   ; Velocity generation is on
comm_mode  = ANGULAR


​however i get LINCS warning and also the log file says this :

​Your simulation settings would have triggered the efficient all-vs-all
kernels in GROMACS 4.5, but these have not been implemented in GROMACS
4.6. Also, we can't use the accelerated SIMD kernels here because
of an unfixed bug. The reference C kernels are correct, though, so
we are proceeding by disabling all CPU architecture-specific
(e.g. SSE2/SSE4/AVX) routines. If performance is important, please
use GROMACS 4.5.7 or try cutoff-scheme = Verlet.

kindly suggest something ..

-- 
Best
*,*
Antara

--
J.R.F.(Project)
Systems Biology Group
CSIR - Institute of Genomics  Integrative Biology
South Campus, New Delhi-110020
M:+91-9717970040
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[gmx-users] error in grompp : Something is wrong in the coordinate formatting of file system.gro

2015-03-16 Thread Antara mazumdar
Hi,
I am trying to minimise a coarse grained system having DOPC lipid bilayer,
a dimeric protein and water. The mdp file has DOPC, Protein and W as
coupling groups and my topology file also mentions the number of each
correctly. However while running grompp i am getting *Something is wrong in
the coordinate formatting of file system.gro* error. No such molecule type
error does not come now.

-- 

*Best,*
*Antara*

--
J.R.F.(Project)
Systems Biology Group
CSIR - Institute of Genomics  Integrative Biology
South Campus, New Delhi-110020
M:+91-9717970040
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[gmx-users] error in grompp : No such molecule type Protein

2015-03-16 Thread Antara mazumdar
Hi,
I am trying to minimise a coarse grained system having DOPC lipid bilayer,
a dimeric protein and water. The mdp file has DOPC, Protein and W as
coupling groups and my topology file also mentions the number of each
correctly. However while running grompp i am getting No such molecule type
Protein error.

-- 

*Best,*
*Antara*

--
J.R.F.(Project)
Systems Biology Group
CSIR - Institute of Genomics  Integrative Biology
South Campus, New Delhi-110020
M:+91-9717970040
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[gmx-users] query regarding coarse grained simulation of a peripheral membrane protein

2015-03-13 Thread Antara mazumdar
​Hi,
How do i generate a topology file of a peripherally attached dimeric
protein with a homogenous lipid bilayer using coarse grained approach? ​i
have concatenated the coarse grained structure of lipids and protein prior
to this.

-- 

*Best,*
*Antara*

--
J.R.F.(Project)
Systems Biology Group
CSIR - Institute of Genomics  Integrative Biology
South Campus, New Delhi-110020
M:+91-9717970040
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[gmx-users] Need of mdp files

2015-02-18 Thread Antara mazumdar
Hi,

I am trying to simulate a peripheral membrane protein in a heterogenous
lipid bilayer of DOPC and DOPG using charmm 36 force field in GROMACS. i
need mdp files for NPT, NVT, steep and MD to check whether the conditions i
am using to simulate my system are appropriate or not.

-- 

Regards,

Antara

--
J.R.F.(Project)
Systems Biology Group
CSIR - Institute of Genomics  Integrative Biology
South Campus, New Delhi-110020
M:+91-9717970040
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[gmx-users] Query regarding generation of gaps between lipid molecules after minimisation even after using position restraints

2015-02-09 Thread Antara mazumdar
Hi,
I minimised a heterogenous lipid system of 1464  DOPC and DOPG and applied
position restraints as well as had vdwradii.dat file for genbox step. Yet
after minimisation, there are gaps between the lipid molecules. Pls suggest
a remedy.

-- 

Regards,

Antara

--
J.R.F.(Project)
Systems Biology Group
CSIR - Institute of Genomics  Integrative Biology
South Campus, New Delhi-110020
M:+91-9717970040
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[gmx-users] ERROR OBTAINED FOR NVT OF DOPC AND PROTEIN SIMULATIONS

2015-02-09 Thread Antara mazumdar
​eRROR OBTAINED DURING NVT:

​
Water molecule starting at atom 673675 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
​NVT CONDITIONS WERE :
​

n for B2AR-POPC system
define  = -DPOSRES  ; Protein is position restrained (uses the
posres.itp file information)
; Parameters describing the details of the NVT simulation protocol
integrator  = md; Algorithm (md = molecular dynamics
[leap-frog integrator]; md-vv = md using velocity verlet; sd = stochastic
dynamics)
dt  = 0.002 ; Time-step (ps)
nsteps  = 25; Number of steps to run (0.002 * 25 =
500 ps)

; Parameters controlling output writing
nstxout = 1000  ; Write coordinates to output .trr file
every 2 ps
nstvout = 1000  ; Write velocities to output .trr file
every 2 ps
nstenergy   = 1000  ; Write energies to output .edr file every
2 ps
nstlog  = 1000  ; Write output to .log file every 2 ps

; Parameters describing neighbors searching and details about interaction
calculations
ns_type = grid  ; Neighbor list search method (simple, grid)
nstlist = 5 ; Neighbor list update frequency (after
every given number of steps)
rlist   = 1.2   ; Neighbor list search cut-off distance (nm)
rcoulomb= 1.2   ; Short-range Coulombic interactions
cut-off distance (nm)
rvdw= 1.2   ; Short-range van der Waals cutoff distance
(nm)
pbc = xyz   ; Direction in which to use Perodic
Boundary Conditions (xyz, xy, no)

; Parameters for treating bonded interactions
continuation= no; Whether a fresh start or a continuation
from a previous run (yes/no)
constraint_algorithm = LINCS; Constraint algorithm (LINCS / SHAKE)
constraints = all-bonds ; Which bonds/angles to constrain
(all-bonds / hbonds / none / all-angles / h-angles)
lincs_iter  = 2 ; Number of iterations to correct for
rotational lengthening in LINCS (related to accuracy)
lincs_order = 8 ; Highest order in the expansion of the
constraint coupling matrix (related to accuracy)

; Parameters for treating electrostatic interactions
coulombtype = PME   ; Long range electrostatic interactions
treatment (cut-off, Ewald, PME)
pme_order   = 4 ; Interpolation order for PME (cubic
interpolation is represented by 4)
fourierspacing  = 0.16  ; Maximum grid spacing for FFT grid using
PME (nm)

; Temperature coupling parameters
tcoupl  = V-rescale ; Modified Berendsen thermostat
using velocity rescaling
tc-grps = Protein DOPC SOL_NA   ; Define groups to be coupled
separately to temperature bath
tau_t   = 0.1   0.1 0.1 ; Group-wise coupling time constant
(ps)
ref_t   = 300   300 300 ; Group-wise reference temperature
(K)

; Pressure coupling parameters
pcoupl  = no; Under NVT conditions pressure coupling is
not done

-- 

Regards,

Antara

--
J.R.F.(Project)
Systems Biology Group
CSIR - Institute of Genomics  Integrative Biology
South Campus, New Delhi-110020
M:+91-9717970040
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[gmx-users] Query regarding gaps between lipid molecules in a heterogenous system of 1464 dopc and dopg

2015-02-09 Thread Antara mazumdar
i got the following result after EM of this system of mine.

writing lowest energy coordinates.

Steepest Descents converged to Fmax  1000 in 15280 steps
Potential Energy  = -5.0853170e+06
Maximum force =  9.9438867e+02 on atom 179440
Norm of force =  7.8095098e+00
 Should i go ahead with NVT and NPT? --

Regards,

Antara

--
J.R.F.(Project)
Systems Biology Group
CSIR - Institute of Genomics  Integrative Biology
South Campus, New Delhi-110020
M:+91-9717970040
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