Re: [gmx-users] hydrophobic interactions

[Sudip Das]

Hi Andrew,

1) http://www.gromacs.org/Documentation/How-tos/Tool_Changes_for_5.0 (follow
the 'g_sas' section)

2) You can use gmx_cluster module to do the cluster analysis. The central
frame of the most populated cluster will be the average structure.


Regards,
Sudip Das

PhD Student
C/o. Prof. S. Balasubramanian
Molecular Simulations Lab
Chemistry and Physics of Materials Unit (CPMU)
Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR)
Bangalore, India



On Fri, Dec 28, 2018 at 4:20 PM Andrew Bostick 
wrote:

> Hi all,
>
> I did md simulation of protein-ligand complex using gromacs 5.1.3.
>
> 1) How to investigate hydrophobic interactions between protein and ligand
> during trajectory? Which tool is appropriate for this aim?
>
> 2) How to get an average structure from whole of trajectory?
>
> Best,
> Andrew
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Re: [gmx-users] Complementing the missing resideus of the protein

[Sudip Das]

Hi Chenlin,

You can use molecular dynamics flexible fitting (MDFF or xMDFF) protocol.

https://www.ks.uiuc.edu/Research/mdff/

Regards,
Sudip Das

PhD Student
C/o. Prof. S. Balasubramanian
Molecular Simulations Lab
Chemistry and Physics of Materials Unit (CPMU)
Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR)
Bangalore, India


On Fri, Oct 5, 2018 at 10:24 AM Chenlin Lu  wrote:

> Hello all,
>
>
> I am working on a protein engineering project. A protein mutant (some )
> was obtained and X-ray crystallography was applied to deterine the crystal
> structure. Unfortunately, there are some residues with high overlap
> electrodensity, which means the structure of these residues could not be
> determined. So, my plan is to use MD to analyis the relation of flexibility
> and Amino acis squences for mutant part for further experiment. As a
> reslut, I am wondering if there is some way to complement (or initial
> generate the configuration) the missing part of the protein in order to do
> MD simulation. Could anyone help me? Thx in advance.
>
>
> Best,
> Chenlin
>
> --
>
> Chenlin Lu
>
> Department of Chemical Engineering,
>
> Tsinghua University, Beijing, 100084
>
> Tel: 86-13120180517
>
> Email: luc...@mails.tsinghua.edu.cn
>
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[gmx-users] Average pressure in CG simulation of oil-water system at NAPzT ensemble

[Sudip Das]

Dear All,

I am running a coarse-grained martini (elastic network) simulation at
NAPzT ensemble for an oil-water system containing a protein at the
interface using GROMACS-5.1.4. The system has overall 27,000 atoms
including refined polarizable (v2.2refPOL) water molecules (The Journal of
Chemical Physics *146*, 054501 (2017); https://doi.org/10.1063/1.4974833).
Initially, the protein was kept in the water phase, but it got adsorbed at
the interface after around 0.15 microsecond.

Even though I have set the reference pressure to be 1 bar, the average
pressure from the simulations results to be around -34 bar, even after 1.5
microseconds run.

 Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Pressure   -34.4124  0.01835.1829  -0.102016  (bar)

I have also run the simulations by reducing the tau_p up to 4.0 ps, but I
don't find any improvement. Following same protocol with isotropic pressure
coupling, average pressure turns out to be around 11 bar.

Are these simulations with average pressure away from reference pressure
assumed to be correct to a reasonable extent?

The corresponding .mdp file is given below:

integrator = md
dt= 0.02
nsteps = 11000

nstcomm = 1
comm-mode = Linear
comm-grps = Oil   Protein_Water_Ion

nstxout= 5000   ;[steps] freq to write coordinates
to trajectory
nstvout= 5000   ;[steps] freq to write velocities
to trajectory
;nstfout = 5000   ;[steps] freq to write forces to
trajectory
nstlog  = 5000   ;[steps] freq to write energies to
log file
nstenergy= 5000   ;[steps] freq to write energies to
energy file
energygrps = system;Which energy group(s) to write to disk

cutoff-scheme = Verlet
nstlist  = 20
ns_type   = grid
pbc  = xyz
verlet-buffer-tolerance  = 0.005

coulombtype= PME; for normal MARTINI water, use
'reaction-field'
rcoulomb = 1.1
epsilon_r = 2.5   ; 15 (with normal MARTINI water)
;epsilon_rf   = 0
vdw_type = cutoff
vdw-modifier= Potential-shift-verlet
rvdw = 1.1
DispCorr  = EnerPres   ; account for cut-off vdW scheme

tcoupl=  v-rescale
tc-grps  =  OilProtein_Water_Ion
tau-t  =  1.0   1.0
ref-t   =  300  300

Pcoupl   = parrinello-rahman
Pcoupltype= semiisotropic
tau_p = 12.0; PR barostat is more stable
with larger tau-p, DdJ, 20130422
ref_p  = 1.0   1.0  ; reference pressure, x-y, z
(in bar)
compressibility   = 0  3e-4   ; isothermal compressibility, bar^-1

gen_vel  = no

constraints= none
constraint_algorithm = Lincs
lincs_order= 4
lincs_warnangle= 30


Thanks in advance.

Best regards,
Sudip
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Re: [gmx-users] Calculating the Hydrophobic and Hydrophilic SASA values on GROMACS version 5.1.2

[Sudip Das]

Hi Andrew,
Follow the below link. Hope that helps.

http://www.gromacs.org/Documentation/How-tos/Tool_Changes_for_5.0 (follow
the 'g_sas' section)

Regards,
Sudip

On Wed, Sep 5, 2018 at 9:56 AM Andrew Srimalka Wijesekera <
2014s14...@stu.cmb.ac.lk> wrote:

> Dear all,
>
> I'm currently studying the structural changes and thermodynamic properties
> of a protein structure when binding the ligand. Here I have ran the MD run
> for 50 ns and calculate the SASA value from the gromacs 5.1.2 version.
> According to my knowledge I got only the total SASA value. But I want to
> get the hydrophobic and hydrophilic SASA values seperately from the gromacs
> 5.1.2 version as well. Therefore would you please help me to solve this
> problem.
> Thanks in advance.
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Re: [gmx-users] Gromacs tabulated potentials for CG models

[Sudip Das]

Dear All,

Please find two more files in the attachment which I forgot to attach in my
previous mail in this thread.

Regards,
Sudip



‌

Sudip Das

PhD Student
C/o. Prof. S. Balasubramanian
Molecular Simulations Lab
Chemistry and Physics of Materials Unit (CPMU)
Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR)
Bangalore, India

On Tue, Jun 19, 2018 at 2:27 PM, Sudip Das  wrote:

> Dear All,
>
> I want to use Gromacs to simulate my coarse-grain model. Our group
> developed the coarse-grain parameters for the system of interest. The
> non-bonded parameters are having a different potential form for different
> pairs. I came across a documentation (http://www.gromacs.org/@api/
> deki/files/94/=gromacs_nb.pdf)
> where we can use a different potential form in a simulation. Here I am
> attaching the itp file.
>
> While I am running the NVT equilibration on the system using 4 cores, the
> simulation is running fine, but when I am using the same configuration on
> more than 4 cores, I am getting an error saying that,
>
> Fatal error:
> 1 of the 35535 bonded interactions could not be calculated because some
> atoms involved moved further apart than the multi-body cut-off distance
> (1.4 nm) or the two-body cut-off distance (1.4 nm), see option -rdd, for
> pairs and tabulated bonds also see option -ddcheck
>
> I want to know how to rectify this problem.
>
> Eagerly, waiting for your reply.
>
> Thanks in advanced.
>
> Regards,
> Sudip Das
>
> PhD Student
> C/o. Prof. S. Balasubramanian
> Molecular Simulations Lab
> Chemistry and Physics of Materials Unit (CPMU)
> Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR)
> Bangalore, India
> ‌
>
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[gmx-users] Gromacs tabulated potentials for CG models

[Sudip Das]

Dear All,

I want to use Gromacs to simulate my coarse-grain model. Our group
developed the coarse-grain parameters for the system of interest. The
non-bonded parameters are having a different potential form for different
pairs. I came across a documentation (
http://www.gromacs.org/@api/deki/files/94/=gromacs_nb.pdf)
where we can use a different potential form in a simulation. Here I am
attaching the itp file.

While I am running the NVT equilibration on the system using 4 cores, the
simulation is running fine, but when I am using the same configuration on
more than 4 cores, I am getting an error saying that,

Fatal error:
1 of the 35535 bonded interactions could not be calculated because some
atoms involved moved further apart than the multi-body cut-off distance
(1.4 nm) or the two-body cut-off distance (1.4 nm), see option -rdd, for
pairs and tabulated bonds also see option -ddcheck

I want to know how to rectify this problem.

Eagerly, waiting for your reply.

Thanks in advanced.

Regards,
Sudip Das

PhD Student
C/o. Prof. S. Balasubramanian
Molecular Simulations Lab
Chemistry and Physics of Materials Unit (CPMU)
Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR)
Bangalore, India
‌
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[gmx-users] Two pair_styles for same atomtypes

[Sudip Das]

Hi Gromacs-Users,

Is it possible to use more than one pair potential on one atom type in
gromacs? If it possible please let me know the process and corresponding
information.

Thanks,

Sudip Das

PhD Student
C/o. Prof. S. Balasubramanian
Molecular Simulations Lab
Chemistry and Physics of Materials Unit (CPMU)
Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR)
Bangalore, India
‌
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Re: [gmx-users] Calculation of shape change of a protein during simulation

[Sudip Das]

Dear Joao and Thomas,

Thanks a lot for your kind reply. I am able to calculate the desired
properties by following your answer.

Best regards,
Sudip



‌

Sudip Das

PhD Student
C/o. Prof. S. Balasubramanian
Molecular Simulations Lab
Chemistry and Physics of Materials Unit (CPMU)
Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR)
Bangalore, India

On Wed, Feb 14, 2018 at 10:11 PM, Thomas Evangelidis <teva...@gmail.com>
wrote:

> You can calculate properties describing molecular shape using PLUMED as a
> trajectory post-processing tool. Example input:
>
>
> GROUP
> ATOMS=1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,
> 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
> LABEL=al
>
> GYRATION TYPE=RADIUS ATOMS=al LABEL=rg_al
> GYRATION TYPE=TRACE ATOMS=al LABEL=tr_al
> GYRATION TYPE=GTPC_1 ATOMS=al LABEL=gtpc1_al
> GYRATION TYPE=GTPC_2 ATOMS=al LABEL=gtpc2_al
> GYRATION TYPE=GTPC_3 ATOMS=al LABEL=gtpc3_al
> GYRATION TYPE=ASPHERICITY ATOMS=al LABEL=asph_al
> GYRATION TYPE=ACYLINDRICITY ATOMS=al LABEL=acyl_al
> GYRATION TYPE=KAPPA2 ATOMS=al LABEL=K2_al
> GYRATION TYPE=RGYR_3 ATOMS=al LABEL=g3_al
> GYRATION TYPE=RGYR_2 ATOMS=al LABEL=g2_al
> GYRATION TYPE=RGYR_1 ATOMS=al LABEL=g1_al
>
> PRINT ARG=rg_al,tr_al,gtpc1_al,gtpc2_al,gtpc3_al,asph_al,
> acyl_al,K2_al,g3_al
> ,g2_al,g1_al STRIDE=1 FILE=shape_hsp90
>
>
>
>
>
>
> --
>
> ==
>
> Dr Thomas Evangelidis
>
> Post-doctoral Researcher
> CEITEC - Central European Institute of Technology
> Masaryk University
> Kamenice 5/A35/2S049,
> 62500 Brno, Czech Republic
>
> email: tev...@pharm.uoa.gr
>
>   teva...@gmail.com
>
>
> website: https://sites.google.com/site/thomasevangelidishomepage/
> --
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[gmx-users] Calculation of shape change of a protein during simulation

[Sudip Das]

Dear All,

Is there any way to calculate the change in shape of a protein with respect
to simulation time using GROMACS or VMD? By the use of the word 'shape', I
mean to say 'spherical' or 'elliptical'; or more specifically the value of
eccentricity of the protein wrt simulation time.

My guess is that it can be calculated from the x, y and z components of the
radius of gyration of the protein wrt simulation time. Am I correct?

Thanks in advance.

Best regards,
Sudip


Sudip Das

PhD Student
C/o. Prof. S. Balasubramanian
Molecular Simulations Lab
Chemistry and Physics of Materials Unit (CPMU)
Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR)
Bangalore, India



‌
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Re: [gmx-users] Related to REMD

[Sudip Das]

Hi Ishrat,

As per REMD, you are supposed to generate different .tpr files for
different replicas at their corresponding temperature and simulate
simultaneously all the replicas. As for example, if you are having 5
replicas,

replica:  0   1 234
temp:300305312322335

Have a look into GROMACS REMD tutorial.

Regards,
Sudip

‌

Sudip Das

PhD Student
C/o. Prof. S. Balasubramanian
Molecular Simulations Lab
Chemistry and Physics of Materials Unit (CPMU)
Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR)
Bangalore, India

On Thu, Jan 4, 2018 at 12:20 PM, ISHRAT JAHAN <jishra...@gmail.com> wrote:

> Hi Sudip
> For doing REMD,I have generated the five seed conformation using trjconv
> command. I have taken only 10 temperature from the temperature generating
> tool, now i want to know whether i have to generate different .tpr file
> using one conformation at all temperature or all conformations at all
> temperature. Will you please tell me what to do as i am unable to
> understand?
> Thanks in advance
>
>
> On Tue, Jan 2, 2018 at 4:55 PM, Sudip Das <das.sudi...@gmail.com> wrote:
>
> > Hi Ishrat,
> >
> >
> > On Tue, Jan 2, 2018 at 4:14 PM, ISHRAT JAHAN <jishra...@gmail.com>
> wrote:
> >
> > > Dear all,
> > > I am trying to do REMD simulation. I had equillbrated the system for
> 5ns
> > > and extracted the seed conformation at 3ns using the command-
> > > gmx trjconv -f traj.trr -o 3ns.gro -s topol.tpr -dump 3000 -pbc mol
> > > I had used temperature generator for REMD simulation from
> > > folding.bmc.uu.se/remd with transition probability of 0.25 in
> > temperature
> > > range of 290-400K.it gives too many replica and i want only 10 replica.
> >
> > will anyone tell me what criteria should be taken for taking 10 replicas
> > >
> >
> > It seems that your system size is reasonably large. You can try using
> > replica exchange with solute scaling (REST2 method) which is basically
> > comes under Hamiltonian replica exchange. It will reduce the number of
> > replicas by scaling the potential energy surface with respect to
> effective
> > temperature of the corresponding replica.
> >
> >
> > > and also tell how to extract the one seed conformation from multiple
> seed
> > > conformation which i had generated using above command.
> > >
> >
> > See the several options under the module trjconv by typing the command:
> > gmx trjconv -h
> >
> >
> > Regards,
> > Sudip
> >
> >
> > Thanks in advance
> > > --
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> > >
> >
> > ‌
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Re: [gmx-users] Related to REMD

[Sudip Das]

Hi Ishrat,


On Tue, Jan 2, 2018 at 4:14 PM, ISHRAT JAHAN  wrote:

> Dear all,
> I am trying to do REMD simulation. I had equillbrated the system for 5ns
> and extracted the seed conformation at 3ns using the command-
> gmx trjconv -f traj.trr -o 3ns.gro -s topol.tpr -dump 3000 -pbc mol
> I had used temperature generator for REMD simulation from
> folding.bmc.uu.se/remd with transition probability of 0.25 in temperature
> range of 290-400K.it gives too many replica and i want only 10 replica.

will anyone tell me what criteria should be taken for taking 10 replicas
>

It seems that your system size is reasonably large. You can try using
replica exchange with solute scaling (REST2 method) which is basically
comes under Hamiltonian replica exchange. It will reduce the number of
replicas by scaling the potential energy surface with respect to effective
temperature of the corresponding replica.


> and also tell how to extract the one seed conformation from multiple seed
> conformation which i had generated using above command.
>

See the several options under the module trjconv by typing the command:
gmx trjconv -h


Regards,
Sudip


Thanks in advance
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Re: [gmx-users] Hydrophobic and hydrophilic SASA for a particular portion of a protein

[Sudip Das]

Hi Justin,

Thanks a lot for your reply!! I got my answer from that link.

Best wishes,
Sudip



‌

Sudip Das

PhD Student
C/o. Prof. S. Balasubramanian
Molecular Simulations Lab
Chemistry and Physics of Materials Unit (CPMU)
Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR)
Bangalore, India

On Thu, Dec 14, 2017 at 1:09 AM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 12/13/17 1:40 PM, Sudip Das wrote:
>
>> Hi Justin,
>>
>> Thanks again for your valuable time!
>>
>> The sasa output file I got contains only two columns (time and sasa).
>>
>> The output coordinate for protein is matching neither with the reference
>> coordinate (from .tpr file), nor with the first or last frame.
>>
>> I am using the following command:
>>
>> gmx_mpi sasa -f traj.xtc -s topol.tpr -n index.ndx -o sasa -q surface.pdb
>> -surface
>>
>> Am I doing something wrong?
>>
>
> http://www.gromacs.org/Documentation/How-tos/Tool_Changes_
> for_5.0?highlight=tool+changes+for+5.0#g_sas
>
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
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Re: [gmx-users] Hydrophobic and hydrophilic SASA for a particular portion of a protein

[Sudip Das]

Hi Justin,

Thanks again for your valuable time!

The sasa output file I got contains only two columns (time and sasa).

The output coordinate for protein is matching neither with the reference
coordinate (from .tpr file), nor with the first or last frame.

I am using the following command:

gmx_mpi sasa -f traj.xtc -s topol.tpr -n index.ndx -o sasa -q surface.pdb
-surface

Am I doing something wrong?


Best wishes,
Sudip



‌

Sudip Das

PhD Student
C/o. Prof. S. Balasubramanian
Molecular Simulations Lab
Chemistry and Physics of Materials Unit (CPMU)
Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR)
Bangalore, India

On Wed, Dec 13, 2017 at 11:23 PM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 12/13/17 12:50 PM, Sudip Das wrote:
>
>> Dear Justin,
>>
>> Thanks for your reply!
>>
>> As you said, I checked with gmx sasa. But it is giving total SASA for the
>> selected region of protein, not the hydrophobic and hydrophilic part of
>> the
>> total SASA for that region. To get it, do I have to use some flags
>> available with gmx sasa?
>>
>
> The output should be a multi-column file, IIRC, but it has been years
> since I've used it.
>
> I have one more query. When I specified -surface flag with gmx sasa, I got
>> the coordinate for the protein together with the coordinate for surface
>> area as dotted point. I have done this calculation over 50 to 100 ns of my
>> simulation trajectory. Is the generated coordinate for protein
>> (together with the coordinate for dotted surface area) averaged over all
>> the frames within 50 to 100ns?
>>
>
> I assume it's just pulling the reference coordinates from the .tpr file,
> but you'd have to check the code to see what it's doing to be sure.
>
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
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Re: [gmx-users] Hydrophobic and hydrophilic SASA for a particular portion of a protein

[Sudip Das]

Dear Rahul,

Thanks for your reply!

Best wishes,
Sudip



‌

Sudip Das

PhD Student
C/o. Prof. S. Balasubramanian
Molecular Simulations Lab
Chemistry and Physics of Materials Unit (CPMU)
Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR)
Bangalore, India

On Wed, Dec 13, 2017 at 9:56 PM, RAHUL SURESH <drrahulsur...@gmail.com>
wrote:

> Hi Sudip
>
> I am not sure if you can do that for the entire trajectory but for a pdb
> structure at particular ns you can calculate the hydrophobicity of
> particular part of protein using Discovery studio.(You have to adopt some
> backbench tricks)
>
> Thank you
>
> On Wed, Dec 13, 2017 at 9:52 PM, Sudip Das <das.sudi...@gmail.com> wrote:
>
> > Dear All,
> >
> > Is there any tool available that can calculate hydrophobic and
> hydrophilic
> > (solvent accessible) surface areas *for a particular portion (not the
> > whole)* of a protein?
> >
> > Thanks in advance!
> >
> > Best wishes,
> >
> > Sudip Das
> >
> > PhD Student
> > C/o. Prof. S. Balasubramanian
> > Molecular Simulations Lab
> > Chemistry and Physics of Materials Unit (CPMU)
> > Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR)
> > Bangalore, India
> >
> >
> >
> > ‌
> > --
> > 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.
>
>
>
>
> --
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
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Re: [gmx-users] Hydrophobic and hydrophilic SASA for a particular portion of a protein

[Sudip Das]

Dear Justin,

Thanks for your reply!

As you said, I checked with gmx sasa. But it is giving total SASA for the
selected region of protein, not the hydrophobic and hydrophilic part of the
total SASA for that region. To get it, do I have to use some flags
available with gmx sasa?

I have one more query. When I specified -surface flag with gmx sasa, I got
the coordinate for the protein together with the coordinate for surface
area as dotted point. I have done this calculation over 50 to 100 ns of my
simulation trajectory. Is the generated coordinate for protein
(together with the coordinate for dotted surface area) averaged over all
the frames within 50 to 100ns?

Thanks again for your valuable time.

Best wishes,
Sudip


‌

Sudip Das

PhD Student
C/o. Prof. S. Balasubramanian
Molecular Simulations Lab
Chemistry and Physics of Materials Unit (CPMU)
Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR)
Bangalore, India

On Wed, Dec 13, 2017 at 10:12 PM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 12/13/17 11:22 AM, Sudip Das wrote:
>
>> Dear All,
>>
>> Is there any tool available that can calculate hydrophobic and hydrophilic
>> (solvent accessible) surface areas *for a particular portion (not the
>> whole)* of a protein?
>>
>
> Yes, you can get that from gmx sasa. Generate a surface for the whole
> protein, and choose whatever subset of that surface that you want as the
> output.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
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[gmx-users] Hydrophobic and hydrophilic SASA for a particular portion of a protein

[Sudip Das]

Dear All,

Is there any tool available that can calculate hydrophobic and hydrophilic
(solvent accessible) surface areas *for a particular portion (not the
whole)* of a protein?

Thanks in advance!

Best wishes,

Sudip Das

PhD Student
C/o. Prof. S. Balasubramanian
Molecular Simulations Lab
Chemistry and Physics of Materials Unit (CPMU)
Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR)
Bangalore, India



‌
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[gmx-users] gmx sasa

[Sudip Das]

Dear All,

I am using 'gmx_mpi sasa' module as below:

gmx_mpi sasa -f traj_0-100ns.xtc -s topol.tpr -o sasa -or res_sasa -q
surface.pdb -surface -b 5

Now, surface.pdb file will generate the surface of the selected portion
together with the coordinates of all the atoms present in the protein. Are
the coordinates of all atoms of the protein averaged over the selected
range of trajectory or they are averaged over the range of trajectory
supplied in the .xtc file (as for example, here, I have selected 50-100 ns,
though my .xtc file ranges from 0-100 ns)?
‌
Thanks in advanced!

Best wishes,
Sudip
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[gmx-users] gmx sasa

[Sudip Das]

Dear All,

I am using 'gmx_mpi sasa' module as below:

gmx_mpi sasa -f traj_0-100ns.xtc -s topol.tpr -o sasa -or res_sasa -q
surface.pdb -surface -b 5

Now, surface.pdb file will generate the surface of the selected portion
together with the coordinates of all the atoms present in the protein. Are
the coordinates of all atoms of the protein averaged over the selected
range of trajectory or they are averaged over the range of trajectory
supplied in the .xtc file (as for example, here, I have selected 50-100 ns,
though my .xtc file ranges from 0-100 ns)?
‌
Thanks in advanced!

Best wishes,
Sudip
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Re: [gmx-users] RDF from NPT simulation?

[Sudip Das]

Dear Justin,

Should I have to use any flag(s) with 'rdf' module to scale the coordinates
for fixing the box size? I didn't find such flag in 'rdf' module.

Please help.

Regards,
Sudip

On Thu, Nov 2, 2017 at 4:41 PM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 11/2/17 6:39 AM, Sudip Das wrote:
>
>> Dear All,
>>
>> Is it possible to calculate RDF from GROMACS module 'rdf' from a NPT
>> simulation trajectory (where box size changes from frame to frame)?
>>
> Yes.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
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[gmx-users] RDF from NPT simulation?

[Sudip Das]

Dear All,

Is it possible to calculate RDF from GROMACS module 'rdf' from a NPT
simulation trajectory (where box size changes from frame to frame)?

Thanks in advance.

Regards,
Sudip
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Re: [gmx-users] CG to AA backmapping: problem in using initram.sh script

[Sudip Das]

Hi Peter,

The path of my mapping file is: /home/CG2AA/Mapping/det.gromos.map

The structural sequence of my detergent is: HO-(CH2-CH2-O)8-(CH2)11-CH3
 (Basically a C12EO8, i.e., polyethylene-glycol (PEG) with C12 hydrophobic
tail).

The content of det.gromos.map file is as below:

[ molecule ]
DET

[ martini ]
OH  O11  O12  O13  O14  O15  O16  O17  O18  C1 C2 C3

[ mapping ]
gromos54a7

[ atoms ]
1   H OH
2   OAOH
3   CH2   O11
4   CH2   O11
5   OEO11
6   CH2   O12
7   CH2   O12
8   OEO12
9   CH2   O13
   10   CH2   O13
   11   OEO13
   12   CH2   O14
   13   CH2   O14
   14   OEO14
   15   CH2   O15
   16   CH2   O15
   17   OEO15
   18   CH2   O16
   19   CH2   O16
   20   OEO16
   21   CH2   O17
   22   CH2   O17
   23   OEO17
   24   CH2   O18
   25   CH2   O18
   26   OEO18
   27   CH2   C1
   28   CH2   C1
   29   CH2   C1
   30   CH2   C1
   31   CH2   C2
   32   CH2   C2
   33   CH2   C2
   34   CH2   C2
   35   CH2   C3
   36   CH2   C3
   37   CH2   C3
   38   CH3   C3


Thanks for your kind and prompt reply!

Best regards,
Sudip




On Mon, Jul 17, 2017 at 3:15 PM, Peter Kroon <p.c.kr...@rug.nl> wrote:

> Hi Sudip,
>
>
> what's the path and content of your DET mapping file?
>
>
> Peter
>
>
> On 17-07-17 11:41, Sudip Das wrote:
> > Dear All,
> >
> > I forgot to mention one point in my previous mail.
> >
> > With the system containing only one detergent molecules gives me the
> > following error, without generating any output file.
> >
> > Residues defined for transformation from martini to gromos54a7:
> > []
> > Traceback (most recent call last):
> >   File "/home/CG2AA/backward1/backward.py", line 821, in 
> > raise ValueError, "Unknown residue: %s\n"%resn
> > ValueError: Unknown residue: DET
> >
> >
> > Best regards,
> > Sudip
> >
> >
> >
> > On Mon, Jul 17, 2017 at 3:04 PM, Sudip Das <das.sudi...@gmail.com>
> wrote:
> >
> >> Dear All,
> >>
> >> I have carried out CGMD simulation of my system consist of a protein
> along
> >> with 30 detergent molecules. I have used Martini parameters along with
> the
> >> ELNEDYN model for protein.
> >>
> >> Now I am trying to get back AA coordinates from the CG structure using
> >> initram.sh script together with GROMACS 5.0.5 (double precision) with
> the
> >> below execution command:
> >>
> >> ./initram.sh -f CG.gro -o AA_gromos.gro -from martini -to gromos54a7 -p
> >> AA.top
> >>
> >> It can find out the dependencies:
> >>
> >> Checking dependencies:
> >> backward.py ... /home/CG2AA/backward.py
> >> gmx_mpi_d ... /home/sudip/softwares/gromacs-5.0.5/build/bin/gmx_mpi_d
> >>
> >>
> >> Even though this gives me the following errors:
> >>
> >> Error reading amber to martini mapping for GMO (file:
> >> /home/CG2AA/Mapping/sol.gromos.map).
> >> .
> >> .
> >> .
> >> Fatal error:
> >> number of coordinates in coordinate file (0-backward.gro, 107331)
> >>  does not match topology (backmapped.top, 108471)
> >>
> >> Now, 108471 - 107331 = 1140, which is same as the number of atoms in 30
> >> detergent molecules.
> >>
> >> In the 0-backward.gro file, coordinates for protein, water and ions are
> >> written, but coordinates for detergent are absent even though the
> >> initram.sh script can find out the detergent mapping scheme (DET) within
> >> the /Mapping directory.
> >>
> >> Residues defined for transformation from martini to gromos54a7:
> >> ['POPC', 'GLN', 'ILE', 'POPE', *'DET*', 'POPS', 'GLY', 'GLU', 'CYS',
> >> 'HIS', 'SER', 'SEP', 'PRO', 'CHOL', 'CL4', 'ASN', 'HEP', 'VAL', 'DOPE',
> >> 'DPPC', 'DOPC', 'THR', 'ASP', 'TRP', 'LYS', 'PHE', 'ALA', 'MET', 'LEU',
> >> 'ARG', 'TYR']
> >>
> >> I want to transform coordinates from Martini to gromos. Then why does
> the
> >> error message "Error reading amber to martini mapping for GMO" tell
> about
> >> amber?
> >>
> >> I have also tried the same protocol with only one detergent molecule as
> my
> >> system. But, still I got the same error.
> >>
> >> Please help me to resolve this.
> >>
> >> Thanks in advance for your kind help.
> >>
> >> N.B.: I have registered in the cgmartini site, but I am unable to find
> out
> >> how to post a query there. So I have posted here. Sorry!
> >>

Re: [gmx-users] CG to AA backmapping: problem in using initram.sh script

[Sudip Das]

Dear All,

I forgot to mention one point in my previous mail.

With the system containing only one detergent molecules gives me the
following error, without generating any output file.

Residues defined for transformation from martini to gromos54a7:
[]
Traceback (most recent call last):
  File "/home/CG2AA/backward1/backward.py", line 821, in 
raise ValueError, "Unknown residue: %s\n"%resn
ValueError: Unknown residue: DET


Best regards,
Sudip



On Mon, Jul 17, 2017 at 3:04 PM, Sudip Das <das.sudi...@gmail.com> wrote:

> Dear All,
>
> I have carried out CGMD simulation of my system consist of a protein along
> with 30 detergent molecules. I have used Martini parameters along with the
> ELNEDYN model for protein.
>
> Now I am trying to get back AA coordinates from the CG structure using
> initram.sh script together with GROMACS 5.0.5 (double precision) with the
> below execution command:
>
> ./initram.sh -f CG.gro -o AA_gromos.gro -from martini -to gromos54a7 -p
> AA.top
>
> It can find out the dependencies:
>
> Checking dependencies:
> backward.py ... /home/CG2AA/backward.py
> gmx_mpi_d ... /home/sudip/softwares/gromacs-5.0.5/build/bin/gmx_mpi_d
>
>
> Even though this gives me the following errors:
>
> Error reading amber to martini mapping for GMO (file:
> /home/CG2AA/Mapping/sol.gromos.map).
> .
> .
> .
> Fatal error:
> number of coordinates in coordinate file (0-backward.gro, 107331)
>  does not match topology (backmapped.top, 108471)
>
> Now, 108471 - 107331 = 1140, which is same as the number of atoms in 30
> detergent molecules.
>
> In the 0-backward.gro file, coordinates for protein, water and ions are
> written, but coordinates for detergent are absent even though the
> initram.sh script can find out the detergent mapping scheme (DET) within
> the /Mapping directory.
>
> Residues defined for transformation from martini to gromos54a7:
> ['POPC', 'GLN', 'ILE', 'POPE', *'DET*', 'POPS', 'GLY', 'GLU', 'CYS',
> 'HIS', 'SER', 'SEP', 'PRO', 'CHOL', 'CL4', 'ASN', 'HEP', 'VAL', 'DOPE',
> 'DPPC', 'DOPC', 'THR', 'ASP', 'TRP', 'LYS', 'PHE', 'ALA', 'MET', 'LEU',
> 'ARG', 'TYR']
>
> I want to transform coordinates from Martini to gromos. Then why does the
> error message "Error reading amber to martini mapping for GMO" tell about
> amber?
>
> I have also tried the same protocol with only one detergent molecule as my
> system. But, still I got the same error.
>
> Please help me to resolve this.
>
> Thanks in advance for your kind help.
>
> N.B.: I have registered in the cgmartini site, but I am unable to find out
> how to post a query there. So I have posted here. Sorry!
>
>
> Best regards,
> Sudip
>
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[gmx-users] CG to AA backmapping: problem in using initram.sh script

[Sudip Das]

Dear All,

I have carried out CGMD simulation of my system consist of a protein along
with 30 detergent molecules. I have used Martini parameters along with the
ELNEDYN model for protein.

Now I am trying to get back AA coordinates from the CG structure using
initram.sh script together with GROMACS 5.0.5 (double precision) with the
below execution command:

./initram.sh -f CG.gro -o AA_gromos.gro -from martini -to gromos54a7 -p
AA.top

It can find out the dependencies:

Checking dependencies:
backward.py ... /home/CG2AA/backward.py
gmx_mpi_d ... /home/sudip/softwares/gromacs-5.0.5/build/bin/gmx_mpi_d


Even though this gives me the following errors:

Error reading amber to martini mapping for GMO (file:
/home/CG2AA/Mapping/sol.gromos.map).
.
.
.
Fatal error:
number of coordinates in coordinate file (0-backward.gro, 107331)
 does not match topology (backmapped.top, 108471)

Now, 108471 - 107331 = 1140, which is same as the number of atoms in 30
detergent molecules.

In the 0-backward.gro file, coordinates for protein, water and ions are
written, but coordinates for detergent are absent even though the
initram.sh script can find out the detergent mapping scheme (DET) within
the /Mapping directory.

Residues defined for transformation from martini to gromos54a7:
['POPC', 'GLN', 'ILE', 'POPE', *'DET*', 'POPS', 'GLY', 'GLU', 'CYS', 'HIS',
'SER', 'SEP', 'PRO', 'CHOL', 'CL4', 'ASN', 'HEP', 'VAL', 'DOPE', 'DPPC',
'DOPC', 'THR', 'ASP', 'TRP', 'LYS', 'PHE', 'ALA', 'MET', 'LEU', 'ARG',
'TYR']

I want to transform coordinates from Martini to gromos. Then why does the
error message "Error reading amber to martini mapping for GMO" tell about
amber?

I have also tried the same protocol with only one detergent molecule as my
system. But, still I got the same error.

Please help me to resolve this.

Thanks in advance for your kind help.

N.B.: I have registered in the cgmartini site, but I am unable to find out
how to post a query there. So I have posted here. Sorry!


Best regards,
Sudip
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Re: [gmx-users] CGMD simulation is not running with antifreeze water beads and 20 fs timestep

[Sudip Das]

Hi Peter,

Sorry for the delay. According to your suggestion, I have equilibrated my
system with gradually increasing time step (1, 2, 5, 10, 15, 20 fs). After
that, the production step is running successfully.

Thanks a lot for your kind help!

Best regards,
Sudip

On Thu, Jun 29, 2017 at 2:32 PM, Peter Kroon <p.c.kr...@rug.nl> wrote:

> Hi Sudip,
>
>
> we had a short discussion over coffee. We also get these warnings, but
> they don't generally lead to significant instabilities. This means you
> probably have an equilibration issue. Could you try equilibrating your
> system with increasing timesteps? So first equilibrate with 5fs, then
> continue with 10 fs, 15fs and finally 20 fs.
>
> If that doesn't work, could you give a more detailed description of your
> system?
>
>
> Peter
>
>
> On 29-06-17 10:07, Peter Kroon wrote:
> > Hi Sudip,
> >
> >
> > there's a dedicated forum for these Martini questions on cgmartini.nl.
> > Recently there was a similar question there
> > (http://cgmartini.nl/index.php/component/kunena/7-mdp-
> options/5491-gpu-verlet-oscillational-period#7308).
> >
> > To summarize, the bonds between the backbone beads are extremely stiff.
> > If your protein is small/short enough you can change them to
> > constraints. I'll start a discussion in the group here on how to handle
> > it further.
> >
> >
> > Peter
> >
> >
> > On 29-06-17 09:06, Sudip Das wrote:
> >> Dear All,
> >>
> >> I am running a CGMD simulation of protein and surfactant in water with
> >> Martini2.0 force field for surfactant and water and ELNEDYN2.2 force
> field
> >> for protein.
> >>
> >> The system is running fine with 20 fs integration timestep. But it
> leads to
> >> solid phase of water. So, I have introduce antifreeze water beads (which
> >> are 10% in number w.r.t. the total number of water beads). But after
> this,
> >> simulation is not at all running with 20 fs timestep and gives the
> error:
> >>
> >> segmentation fault (signal 11)
> >>
> >> Within output file, it shows:
> >>
> >> Step 2, time 0.04 (ps)  LINCS WARNING
> >> relative constraint deviation after LINCS:
> >> rms 0.007237, max 0.028381 (between atoms 20 and 21)
> >> bonds that rotated more than 30 degrees:
> >>  atom 1 atom 2  angle  previous, current, constraint length
> >>  20 21   30.40.1981   0.1895  0.1950
> >>
> >>
> >> I have tried to solve it in several ways, i.e., decreasing the time
> steps
> >> (it is running fine with 2 fs), equilibrating the system properly,
> >> compiling and running in serial version of gromacs (to test whether the
> >> error comes due to domain decomposition during parallel run) etc. Even
> >> though, I am getting the same error.
> >>
> >> While compiling the job with grompp, I got the below warning:
> >>
> >> WARNING 1 [file system.top, line 18]:
> >>   The bond in molecule-type Protein_A between atoms 1 BB and 2 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.
> >>
> >> But, following the link
> >> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-
> users/2014-May/089120.html
> >> , I have ignored this warning using -maxwarn flag. Probably this
> wouldn't
> >> be the cause for this error, as I got exactly the same warning for the
> >> system without antifreeze water beads.
> >>
> >>
> >> Please help me to solve this problem. I would be happy to share my
> files if
> >> needed.
> >>
> >> Thanks in advance!
> >>
> >> Best regards.
> >> Sudip
> >
>
>
>
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[gmx-users] CGMD simulation is not running with antifreeze water beads and 20 fs timestep

[Sudip Das]

Dear All,

I am running a CGMD simulation of protein and surfactant in water with
Martini2.0 force field for surfactant and water and ELNEDYN2.2 force field
for protein.

The system is running fine with 20 fs integration timestep. But it leads to
solid phase of water. So, I have introduce antifreeze water beads (which
are 10% in number w.r.t. the total number of water beads). But after this,
simulation is not at all running with 20 fs timestep and gives the error:

segmentation fault (signal 11)

Within output file, it shows:

Step 2, time 0.04 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.007237, max 0.028381 (between atoms 20 and 21)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
 20 21   30.40.1981   0.1895  0.1950


I have tried to solve it in several ways, i.e., decreasing the time steps
(it is running fine with 2 fs), equilibrating the system properly,
compiling and running in serial version of gromacs (to test whether the
error comes due to domain decomposition during parallel run) etc. Even
though, I am getting the same error.

While compiling the job with grompp, I got the below warning:

WARNING 1 [file system.top, line 18]:
  The bond in molecule-type Protein_A between atoms 1 BB and 2 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.

But, following the link
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-May/089120.html
, I have ignored this warning using -maxwarn flag. Probably this wouldn't
be the cause for this error, as I got exactly the same warning for the
system without antifreeze water beads.


Please help me to solve this problem. I would be happy to share my files if
needed.

Thanks in advance!

Best regards.
Sudip
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[gmx-users] Is dssp required with CG ElNeDyn model?

[Sudip Das]

Dear All,

I am trying to set up a system containing protein in water
using coarse-grained ElNeDyn model in GROMACS. As this model itself
considers a global elastic network between the backbone beads to conserve
the conformation, *is it necessary to use -dssp option* while generating CG
structure and topolgy for the protein using martinize.py script?

Thanks in advance...

Regards,
Sudip
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Re: [gmx-users] How to install g_fg2cg

[Sudip Das]

Hi Peter,

Thanks for your useful inputs.

Regards,
Sudip




On Wed, Apr 12, 2017 at 2:42 PM, Peter Kroon <p.c.kr...@rug.nl> wrote:

> Hi Sudip,
>
>
> as far as I know, fg2cg is extremely old and no longer maintained. I
> would suggest you look at other tools. In particular, Backwards [1] and
> pyCGtool [2] spring to mind.
>
>
> Peter
>
>
> [1] http://cgmartini.nl/index.php/tools2/resolution-transformation
>
> [2] https://github.com/jag1g13/pycgtool
>
>
> On 12-04-17 11:04, Sudip Das wrote:
> > Dear All,
> >
> > I have atomistic (fine-grained) coordinate for a molecule. I also have
> all
> > atom as well as coarse-grained (CG) topology parameters for that
> molecule.
> > Now to perform a CG simulation run for the molecule, the only thing that
> I
> > need to have is a CG coordinate file for this molecule.
> >
> > Probably *g_fg2cg* gromacs tool can help me to do this. But *how to
> install*
> > this tool within GROMACS 5.x? Please help me to resolve this.
> >
> >
> > Thanks in advance.
> >
> >
> > Best regards,
> > Sudip
>
>
>
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[gmx-users] How to install g_fg2cg

[Sudip Das]

Dear All,

I have atomistic (fine-grained) coordinate for a molecule. I also have all
atom as well as coarse-grained (CG) topology parameters for that molecule.
Now to perform a CG simulation run for the molecule, the only thing that I
need to have is a CG coordinate file for this molecule.

Probably *g_fg2cg* gromacs tool can help me to do this. But *how to install*
this tool within GROMACS 5.x? Please help me to resolve this.


Thanks in advance.


Best regards,
Sudip
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Re: [gmx-users] Missing bond

[Sudip Das]

Dear Justin,

Thanks for your kind help!

Best regards,
Sudip




On Mon, Apr 3, 2017 at 5:20 PM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 4/1/17 1:18 AM, Sudip Das wrote:
>
>> Dear All,
>>
>> While I am preparing my system topology with pdb2gmx for a system
>> containing enzyme with 30 non-ionic surfactant molecules in water, I got
>> 36
>> number of bonds per surfactant molecules, but actually it has 37 bonds
>> (anyways, the number of angle, dihedral etc. are correct). From the
>> generated topology for this surfactant, I found out the missing bond. But
>> I
>> checked that I have incorporated that bond in aminoacids.rtp file and that
>> bond type is also present in the ffbonded.itp file.
>>
>> To figure out the reason, I used the pdb2gmx for a system with only 30
>> surfactant molecules in water (no enzyme). Again I encountered the same
>> problem.
>>
>> So, what could be the solution? Please assist me.
>>
>>
> Something does not add up.  Angles and dihedrals are built from the bonds,
> so if there's a bond missing, the angles and dihedrals shouldn't be right.
> Which bond is missing?  If it's in the .rtp there's no way it is somehow
> ignored while the others get processed correctly.
>
> -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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[gmx-users] Missing bond

[Sudip Das]

Dear All,

While I am preparing my system topology with pdb2gmx for a system
containing enzyme with 30 non-ionic surfactant molecules in water, I got 36
number of bonds per surfactant molecules, but actually it has 37 bonds
(anyways, the number of angle, dihedral etc. are correct). From the
generated topology for this surfactant, I found out the missing bond. But I
checked that I have incorporated that bond in aminoacids.rtp file and that
bond type is also present in the ffbonded.itp file.

To figure out the reason, I used the pdb2gmx for a system with only 30
surfactant molecules in water (no enzyme). Again I encountered the same
problem.

So, what could be the solution? Please assist me.

Thanks in advanced.


Best regards,
Sudip
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Re: [gmx-users] PLUMED Meeting 2017

[Sudip Das]

Dear users,

Sorry for spamming your inbox. I have unintentionally sent this mail.

Regards,
Sudip




On Mon, Feb 27, 2017 at 9:33 PM, Sudip Das <das.sudi...@gmail.com> wrote:

> Dear Tarakda,
>
> As CCEM meeting is from 15th to 20th May, should I attend this PLUMED
> meeting also (22-27th May)? What do you suggest? Yet I haven't talk to sir
> regarding this.
>
> Regards,
> Sudip
>
>
>
>
> On Mon, Feb 27, 2017 at 9:11 PM, Giovanni Bussi <bu...@sissa.it> wrote:
>
>> Dear all,
>>
>> this meeting might be relevant for gromacs users, so we also post it here.
>>
>> Atomistic simulations play a fundamental and ever-increasing role in
>> biophysics, molecular biology, chemistry, and condensed-matter physics.
>> Unfortunately, the large numbers of particles in realistic systems and the
>> long ranged interactions between the atoms make simulations of
>> biomolecules
>> and technological materials computationally expensive. As a result direct
>> simulation can only be used to examine process that occur on relatively
>> short-time scales. The direct study of rare events such as protein
>> folding,
>> drug binding, chemical reactions and phase transitions is too much of a
>> computational challenge in many cases of interest. To extend the time
>> scales which can be investigated by atomistic simulations, several
>> powerful
>> enhanced-sampling methods have been developed in recent years. In
>> addition,
>> numerous analysis strategies have been developed to better exploit what
>> can
>> be learnt from short simulations.
>>
>> Traditionally, ad-hoc implementations of these analysis and biasing
>> methods
>> have been written and used by their developers. In many cases these
>> implementations have not been distributed to the wider community.
>> Furthermore, they often reflect their developers’ interests and thus have
>> a
>> lack of generalization. In addition, the various codes that have been
>> distributed, often use different conventions in their input files, which
>> is
>> confusing for end users. For these reasons we released a suite of analysis
>> and biasing routines called PLUMED (http://www.plumed.org) in 2009.
>> PLUMED
>> is an open source, freely-available plugin that can be interfaced with
>> some
>> of the most popular molecular dynamics (MD) programs (GROMACS, NAMD,
>> DL_POLY, AMBER, etc.). It allows the user to perform free-energy
>> calculations using state-of-the-art enhanced sampling techniques, such as
>> metadynamics, umbrella sampling, and steered MD. This unified and portable
>> implementation of these enhanced sampling algorithms facilitates
>> comparison
>> between different techniques and between MD engines. In addition, PLUMED
>> can be used to analyze trajectories both in post-processing and on-the-fly
>> during the simulation.
>>
>> On May 22-27, 2017 we are organizing a PLUMED meeting at the Scuola
>> Internazionale di Studi Avanzati (SISSA), Trieste, Italy. The format will
>> be similar to the meeting held in Belfast, UK, in 2014, that is three days
>> of introductory tutorial followed by a three day user meeting. The
>> tutorial
>> will start on Monday 22 in the morning and finish on the afternoon of
>> Wednesday 24. The user meeting will start on the morning of Thursday 25
>> and
>> finish at lunchtime on Saturday 27.
>>
>> There are a limited number of places for students and post-docs that wish
>> to join the meeting. We expect two types of participants:
>>
>>- Students who wish to participate in both the tutorial and the user
>>meeting
>>- More senior participants who wish to only take part in the user
>> meeting
>>
>> We invite all participants to submit an abstract. We will select the
>> participants who will present talks during the user meeting from the
>> abstracts submitted. Those abstracts that are not accepted for talks can
>> be
>> presented during the poster session.
>>
>> It is not necessary to pay any fee for participation in either the
>> tutorial
>> or the user meeting. However, we will only be able to pay for the
>> accommodation of those speakers presenting talks at the user meeting.
>> Furthermore, we will only be able to support three nights (Wednesday to
>> Saturday) of accommodation for these speakers.  We will not be able to
>> provide any financial or logistical support for your trip to Trieste.
>>
>> *The deadline for applications is March 15.* Those candidates admitted to
>> the tutorial, to the user meeting, or

Re: [gmx-users] PLUMED Meeting 2017

[Sudip Das]

Dear Tarakda,

As CCEM meeting is from 15th to 20th May, should I attend this PLUMED
meeting also (22-27th May)? What do you suggest? Yet I haven't talk to sir
regarding this.

Regards,
Sudip




On Mon, Feb 27, 2017 at 9:11 PM, Giovanni Bussi  wrote:

> Dear all,
>
> this meeting might be relevant for gromacs users, so we also post it here.
>
> Atomistic simulations play a fundamental and ever-increasing role in
> biophysics, molecular biology, chemistry, and condensed-matter physics.
> Unfortunately, the large numbers of particles in realistic systems and the
> long ranged interactions between the atoms make simulations of biomolecules
> and technological materials computationally expensive. As a result direct
> simulation can only be used to examine process that occur on relatively
> short-time scales. The direct study of rare events such as protein folding,
> drug binding, chemical reactions and phase transitions is too much of a
> computational challenge in many cases of interest. To extend the time
> scales which can be investigated by atomistic simulations, several powerful
> enhanced-sampling methods have been developed in recent years. In addition,
> numerous analysis strategies have been developed to better exploit what can
> be learnt from short simulations.
>
> Traditionally, ad-hoc implementations of these analysis and biasing methods
> have been written and used by their developers. In many cases these
> implementations have not been distributed to the wider community.
> Furthermore, they often reflect their developers’ interests and thus have a
> lack of generalization. In addition, the various codes that have been
> distributed, often use different conventions in their input files, which is
> confusing for end users. For these reasons we released a suite of analysis
> and biasing routines called PLUMED (http://www.plumed.org) in 2009. PLUMED
> is an open source, freely-available plugin that can be interfaced with some
> of the most popular molecular dynamics (MD) programs (GROMACS, NAMD,
> DL_POLY, AMBER, etc.). It allows the user to perform free-energy
> calculations using state-of-the-art enhanced sampling techniques, such as
> metadynamics, umbrella sampling, and steered MD. This unified and portable
> implementation of these enhanced sampling algorithms facilitates comparison
> between different techniques and between MD engines. In addition, PLUMED
> can be used to analyze trajectories both in post-processing and on-the-fly
> during the simulation.
>
> On May 22-27, 2017 we are organizing a PLUMED meeting at the Scuola
> Internazionale di Studi Avanzati (SISSA), Trieste, Italy. The format will
> be similar to the meeting held in Belfast, UK, in 2014, that is three days
> of introductory tutorial followed by a three day user meeting. The tutorial
> will start on Monday 22 in the morning and finish on the afternoon of
> Wednesday 24. The user meeting will start on the morning of Thursday 25 and
> finish at lunchtime on Saturday 27.
>
> There are a limited number of places for students and post-docs that wish
> to join the meeting. We expect two types of participants:
>
>- Students who wish to participate in both the tutorial and the user
>meeting
>- More senior participants who wish to only take part in the user
> meeting
>
> We invite all participants to submit an abstract. We will select the
> participants who will present talks during the user meeting from the
> abstracts submitted. Those abstracts that are not accepted for talks can be
> presented during the poster session.
>
> It is not necessary to pay any fee for participation in either the tutorial
> or the user meeting. However, we will only be able to pay for the
> accommodation of those speakers presenting talks at the user meeting.
> Furthermore, we will only be able to support three nights (Wednesday to
> Saturday) of accommodation for these speakers.  We will not be able to
> provide any financial or logistical support for your trip to Trieste.
>
> *The deadline for applications is March 15.* Those candidates admitted to
> the tutorial, to the user meeting, or selected to give an oral
> presenteation will be notified by the April 1, so as to have time to
> organize their trip.
>
> All the information, including the application form, can be found at
> http://sites.google.com/view/plumed-meeting-2017/home
> Hoping to see you in Trieste,
>
> Giovanni, Max, Carlo, and Gareth
>
>
> --
> Giovanni Bussi
> Scuola Internazionale Superiore di Studi Avanzati - SISSA
> via Bonomea 265, 34136 Trieste, Italy
> email: bu...@sissa.it
> web:   http://people.sissa.it/~bussi
>   http://srnas.sissa.it
> --
> 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
> 

Re: [gmx-users] Wrong pressure with rigid water

[Sudip Das]

Hi Mark,

The problem is resolved.

Previously, I was using rlist = rvdw = rcoulomb = 1.2, which leads to high
pressure from NVT run. NPT equilibrated avg box length (7.13927 nm) was
used for NVT run.

But I got correct pressure by using rlist = rvdw = rcoulomb = 1.4 (suitable
for GROMOS force field). NPT equilibrated avg box length (7.2115 nm) is
used for NVT run.

Thanks for your kind replies.

Best regards,
Sudip

On Tue, Nov 15, 2016 at 7:05 PM, Sudip Das <das.sudi...@gmail.com> wrote:

> Dear Mark,
>
> I have forgot to mention one point. All the data that are provided in the
> previous mail, are for simulation with rigid water molecules.
>
> Best regards,
> Sudip
>
> On Tue, Nov 15, 2016 at 7:00 PM, Sudip Das <das.sudi...@gmail.com> wrote:
>
>> Dear Mark,
>>
>> Sorry if I misunderstood your point. I am aware that GROMOS force field
>> was parametrized to work with rigid water. My aim is also not to use
>> flexible water. I have performed the flexible water simulation just for
>> testing purpose.
>>
>> Also the box length is converged (with a 0.0005 nm fluctuation) after the
>> NPT equilibration run and I have used this average box length for the NVT
>> production run.
>>
>> In the NPT equilibration, physical quantities like temperature, pressure
>> (fluctuating between 1 to 2 bar), energies are behaving well. The same is
>> also true for NVT production run, except pressure which is fluctuation
>> between 500 to 1000 bar with an average of 750-780 bar.
>>
>> I am confused about what could be the reason of this high pressure
>> although other quantities are behaving well.
>>
>> Thanks in advanced for your kind suggestions.
>>
>> Best regards,
>> Sudip
>>
>> On Tue, Nov 15, 2016 at 6:03 PM, Mark Abraham <mark.j.abra...@gmail.com>
>> wrote:
>>
>>> Hi,
>>>
>>> That's not what I suggested you need to think about. Lots of things go
>>> into
>>> making a useful physical model, and the fact that so far you think the
>>> pressure is OK is only a tiny part of that. You chose a force field that
>>> was parametrized to work with rigid water. If you use it with something
>>> else, then the burden of proof is on you that your eventual observations
>>> will be a valid model.
>>>
>>> Also 750 bar +/- 1000 or with large drift would not be a significant
>>> observation. But only you know these things. Also, you could well have
>>> chosen a volume that is too small because you didn't measure pressure
>>> appropriately during the end of your equilibration phase.
>>>
>>> Mark
>>>
>>> On Tue, Nov 15, 2016 at 1:19 PM Sudip Das <das.sudi...@gmail.com> wrote:
>>>
>>> > Dear Mark,
>>> >
>>> > Thanks for your reply.
>>> >
>>> > As rigid water was not giving reasonable pressure, I have tried with
>>> > flexible one where pressure is behaving well upto 2 ns of NVT
>>> simulation.
>>> >
>>> >
>>> > Here is the details of my system:
>>> >
>>> > System: Protein in water
>>> > # of residues in protein: 188
>>> > # of water molecules: 17876
>>> > # of NA cation: 3
>>> > Box length (after NPT equilibration): 7.13927 nm
>>> >
>>> >
>>> >
>>> > Here is the nvt_production.mdp file:
>>> >
>>> >
>>> > title= Protein-ligand complex NVT production
>>> > ;define  = -DFLEXIBLE
>>> >
>>> > ; Run parameters
>>> > integrator  = md
>>> > nsteps  = 20
>>> > dt  = 0.0005
>>> > nstcomm  = 1
>>> > comm_grps = system
>>> > comm_mode   = linear
>>> >
>>> > ; Output control
>>> > nstxout = 200
>>> > nstvout = 200
>>> > nstenergy = 200
>>> > nstlog   = 200
>>> > energygrps  = system
>>> >
>>> > ; Bond parameters
>>> > continuation= no
>>> > constraints = none
>>> >
>>> > ; Neighborsearching
>>> > ns_type = grid
>>> > nstlist = 5
>>> > rlist   = 1.4
>>> >
>>> > rvdw  = 1.4
>>> > cutoff-scheme = Verlet
>>> > vdwtype   = cut-off
>>> >
>>> > ; Electrostatics
>>> > rcoulomb= 1.4
>>> > coulombtype = PME
>>> > pme

Re: [gmx-users] Wrong pressure with rigid water

[Sudip Das]

Dear Mark,

I have forgot to mention one point. All the data that are provided in the
previous mail, are for simulation with rigid water molecules.

Best regards,
Sudip

On Tue, Nov 15, 2016 at 7:00 PM, Sudip Das <das.sudi...@gmail.com> wrote:

> Dear Mark,
>
> Sorry if I misunderstood your point. I am aware that GROMOS force field
> was parametrized to work with rigid water. My aim is also not to use
> flexible water. I have performed the flexible water simulation just for
> testing purpose.
>
> Also the box length is converged (with a 0.0005 nm fluctuation) after the
> NPT equilibration run and I have used this average box length for the NVT
> production run.
>
> In the NPT equilibration, physical quantities like temperature, pressure
> (fluctuating between 1 to 2 bar), energies are behaving well. The same is
> also true for NVT production run, except pressure which is fluctuation
> between 500 to 1000 bar with an average of 750-780 bar.
>
> I am confused about what could be the reason of this high pressure
> although other quantities are behaving well.
>
> Thanks in advanced for your kind suggestions.
>
> Best regards,
> Sudip
>
> On Tue, Nov 15, 2016 at 6:03 PM, Mark Abraham <mark.j.abra...@gmail.com>
> wrote:
>
>> Hi,
>>
>> That's not what I suggested you need to think about. Lots of things go
>> into
>> making a useful physical model, and the fact that so far you think the
>> pressure is OK is only a tiny part of that. You chose a force field that
>> was parametrized to work with rigid water. If you use it with something
>> else, then the burden of proof is on you that your eventual observations
>> will be a valid model.
>>
>> Also 750 bar +/- 1000 or with large drift would not be a significant
>> observation. But only you know these things. Also, you could well have
>> chosen a volume that is too small because you didn't measure pressure
>> appropriately during the end of your equilibration phase.
>>
>> Mark
>>
>> On Tue, Nov 15, 2016 at 1:19 PM Sudip Das <das.sudi...@gmail.com> wrote:
>>
>> > Dear Mark,
>> >
>> > Thanks for your reply.
>> >
>> > As rigid water was not giving reasonable pressure, I have tried with
>> > flexible one where pressure is behaving well upto 2 ns of NVT
>> simulation.
>> >
>> >
>> > Here is the details of my system:
>> >
>> > System: Protein in water
>> > # of residues in protein: 188
>> > # of water molecules: 17876
>> > # of NA cation: 3
>> > Box length (after NPT equilibration): 7.13927 nm
>> >
>> >
>> >
>> > Here is the nvt_production.mdp file:
>> >
>> >
>> > title= Protein-ligand complex NVT production
>> > ;define  = -DFLEXIBLE
>> >
>> > ; Run parameters
>> > integrator  = md
>> > nsteps  = 20
>> > dt  = 0.0005
>> > nstcomm  = 1
>> > comm_grps = system
>> > comm_mode   = linear
>> >
>> > ; Output control
>> > nstxout = 200
>> > nstvout = 200
>> > nstenergy = 200
>> > nstlog   = 200
>> > energygrps  = system
>> >
>> > ; Bond parameters
>> > continuation= no
>> > constraints = none
>> >
>> > ; Neighborsearching
>> > ns_type = grid
>> > nstlist = 5
>> > rlist   = 1.4
>> >
>> > rvdw  = 1.4
>> > cutoff-scheme = Verlet
>> > vdwtype   = cut-off
>> >
>> > ; Electrostatics
>> > rcoulomb= 1.4
>> > coulombtype = PME
>> > pme_order   = 4
>> > fourierspacing  = 0.16
>> >
>> > ; Temperature coupling
>> > tcoupl  = nose-hoover
>> > tc-grps = system
>> > tau_t   = 1.0
>> > ref_t   = 300
>> >
>> > ; Pressure coupling
>> > pcoupl  = no
>> >
>> > ; Periodic boundary conditions
>> > pbc = xyz
>> >
>> > ; Dispersion correction
>> > DispCorr= EnerPres
>> >
>> > ; Velocity generation
>> > gen_vel = no
>> >
>> >
>> >
>> > Best regards,
>> > Sudip
>> >
>> > On Tue, Nov 15, 2016 at 1:28 PM, Mark Abraham <mark.j.abra...@gmail.com
>> >
>> > wrote:
>> >
>> > > Hi,
>> > >
>> > > The solvent models are designed to be rigid, use flexible versions
>&g

Re: [gmx-users] Wrong pressure with rigid water

[Sudip Das]

Dear Mark,

Sorry if I misunderstood your point. I am aware that GROMOS force field was
parametrized to work with rigid water. My aim is also not to use flexible
water. I have performed the flexible water simulation just for testing
purpose.

Also the box length is converged (with a 0.0005 nm fluctuation) after the
NPT equilibration run and I have used this average box length for the NVT
production run.

In the NPT equilibration, physical quantities like temperature, pressure
(fluctuating between 1 to 2 bar), energies are behaving well. The same is
also true for NVT production run, except pressure which is fluctuation
between 500 to 1000 bar with an average of 750-780 bar.

I am confused about what could be the reason of this high pressure although
other quantities are behaving well.

Thanks in advanced for your kind suggestions.

Best regards,
Sudip

On Tue, Nov 15, 2016 at 6:03 PM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> That's not what I suggested you need to think about. Lots of things go into
> making a useful physical model, and the fact that so far you think the
> pressure is OK is only a tiny part of that. You chose a force field that
> was parametrized to work with rigid water. If you use it with something
> else, then the burden of proof is on you that your eventual observations
> will be a valid model.
>
> Also 750 bar +/- 1000 or with large drift would not be a significant
> observation. But only you know these things. Also, you could well have
> chosen a volume that is too small because you didn't measure pressure
> appropriately during the end of your equilibration phase.
>
> Mark
>
> On Tue, Nov 15, 2016 at 1:19 PM Sudip Das <das.sudi...@gmail.com> wrote:
>
> > Dear Mark,
> >
> > Thanks for your reply.
> >
> > As rigid water was not giving reasonable pressure, I have tried with
> > flexible one where pressure is behaving well upto 2 ns of NVT simulation.
> >
> >
> > Here is the details of my system:
> >
> > System: Protein in water
> > # of residues in protein: 188
> > # of water molecules: 17876
> > # of NA cation: 3
> > Box length (after NPT equilibration): 7.13927 nm
> >
> >
> >
> > Here is the nvt_production.mdp file:
> >
> >
> > title= Protein-ligand complex NVT production
> > ;define  = -DFLEXIBLE
> >
> > ; Run parameters
> > integrator  = md
> > nsteps  = 20
> > dt  = 0.0005
> > nstcomm  = 1
> > comm_grps = system
> > comm_mode   = linear
> >
> > ; Output control
> > nstxout = 200
> > nstvout = 200
> > nstenergy = 200
> > nstlog   = 200
> > energygrps  = system
> >
> > ; Bond parameters
> > continuation= no
> > constraints = none
> >
> > ; Neighborsearching
> > ns_type = grid
> > nstlist = 5
> > rlist   = 1.4
> >
> > rvdw  = 1.4
> > cutoff-scheme = Verlet
> > vdwtype   = cut-off
> >
> > ; Electrostatics
> > rcoulomb= 1.4
> > coulombtype = PME
> > pme_order   = 4
> > fourierspacing  = 0.16
> >
> > ; Temperature coupling
> > tcoupl  = nose-hoover
> > tc-grps = system
> > tau_t   = 1.0
> > ref_t   = 300
> >
> > ; Pressure coupling
> > pcoupl  = no
> >
> > ; Periodic boundary conditions
> > pbc = xyz
> >
> > ; Dispersion correction
> > DispCorr= EnerPres
> >
> > ; Velocity generation
> > gen_vel = no
> >
> >
> >
> > Best regards,
> > Sudip
> >
> > On Tue, Nov 15, 2016 at 1:28 PM, Mark Abraham <mark.j.abra...@gmail.com>
> > wrote:
> >
> > > Hi,
> > >
> > > The solvent models are designed to be rigid, use flexible versions only
> > if
> > > you know why they will be a good model for you.
> > >
> > > Measuring pressure can take nanoseconds, but we don't have enough
> > > information to know what you've done and its error estimates.
> > >
> > > Mark
> > >
> > > On Mon, 14 Nov 2016 17:21 Sudip Das <das.sudi...@gmail.com> wrote:
> > >
> > > > Dear All,
> > > >
> > > > I am simulating a protein in water with GROMOS96 force field
> > (gromos54a7)
> > > > and SPC/E water model. After minimization followed by NVT
> > equilibration,
> > > I
> > > > performed 2ns of NPT equilibration. From the converged box length I
> > have
> > > > taken the average value and set 

Re: [gmx-users] Wrong pressure with rigid water

[Sudip Das]

Dear Mark,

Thanks for your reply.

As rigid water was not giving reasonable pressure, I have tried with
flexible one where pressure is behaving well upto 2 ns of NVT simulation.


Here is the details of my system:

System: Protein in water
# of residues in protein: 188
# of water molecules: 17876
# of NA cation: 3
Box length (after NPT equilibration): 7.13927 nm



Here is the nvt_production.mdp file:


title= Protein-ligand complex NVT production
;define  = -DFLEXIBLE

; Run parameters
integrator  = md
nsteps  = 20
dt  = 0.0005
nstcomm  = 1
comm_grps = system
comm_mode   = linear

; Output control
nstxout = 200
nstvout = 200
nstenergy = 200
nstlog   = 200
energygrps  = system

; Bond parameters
continuation= no
constraints = none

; Neighborsearching
ns_type = grid
nstlist = 5
rlist   = 1.4

rvdw  = 1.4
cutoff-scheme = Verlet
vdwtype   = cut-off

; Electrostatics
rcoulomb= 1.4
coulombtype = PME
pme_order   = 4
fourierspacing  = 0.16

; Temperature coupling
tcoupl  = nose-hoover
tc-grps = system
tau_t   = 1.0
ref_t   = 300

; Pressure coupling
pcoupl  = no

; Periodic boundary conditions
pbc = xyz

; Dispersion correction
DispCorr= EnerPres

; Velocity generation
gen_vel = no



Best regards,
Sudip

On Tue, Nov 15, 2016 at 1:28 PM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> The solvent models are designed to be rigid, use flexible versions only if
> you know why they will be a good model for you.
>
> Measuring pressure can take nanoseconds, but we don't have enough
> information to know what you've done and its error estimates.
>
> Mark
>
> On Mon, 14 Nov 2016 17:21 Sudip Das <das.sudi...@gmail.com> wrote:
>
> > Dear All,
> >
> > I am simulating a protein in water with GROMOS96 force field (gromos54a7)
> > and SPC/E water model. After minimization followed by NVT equilibration,
> I
> > performed 2ns of NPT equilibration. From the converged box length I have
> > taken the average value and set the box length (in npt_equilibrium.gro
> > file) to that value and used this for NVT production run.
> >
> > In the production run, temperature, potential and total energies are
> > reasonable, whereas the pressure is behaving weirdly. I have started the
> > NVT production run with 1 bar pressure.
> >
> >
> > NVT production run with flexible water (define = -DFLEXIBLE): P = 1 to 5
> > bar
> >
> > NVT production run with rigid water: P = 750 to 780 bar
> >
> >
> > Did anyone encountered this kind of problem? I would appreciate your kind
> > help in resolving this.
> >
> > Best regards,
> > Sudip
> > --
> > 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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> > send a mail to gmx-users-requ...@gromacs.org.
> >
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[gmx-users] Wrong pressure with rigid water

[Sudip Das]

Dear All,

I am simulating a protein in water with GROMOS96 force field (gromos54a7)
and SPC/E water model. After minimization followed by NVT equilibration, I
performed 2ns of NPT equilibration. From the converged box length I have
taken the average value and set the box length (in npt_equilibrium.gro
file) to that value and used this for NVT production run.

In the production run, temperature, potential and total energies are
reasonable, whereas the pressure is behaving weirdly. I have started the
NVT production run with 1 bar pressure.


NVT production run with flexible water (define = -DFLEXIBLE): P = 1 to 5 bar

NVT production run with rigid water: P = 750 to 780 bar


Did anyone encountered this kind of problem? I would appreciate your kind
help in resolving this.

Best regards,
Sudip
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[gmx-users] Fwd: Change in dihedral angle

[Sudip Das]

Dear All,

I am performing simulation of a protein containing cyclic peptide ring (not
an regular amino acid) using GROMOS54a7 force field with GROMACS 5.0.5
package. After equilibration and NVT production run, the final structure
having a C-CHn-CHn-C dihedral angle has a value of -18.5 degree, whereas
after optimizing the final structure quantum chemically in Gaussian09
software, the same dihedral angle gives the value equal to +18.1 degree.

Can anyone please suggest any solution? Should I need to change the
dihedral angle parameter in the force field? Or this is just a problem of
sign convention between the above to computing softwares?

Thanks in advanced.

Regards,
Sudip
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Re: [gmx-users] unusual bonds

[Sudip Das]

Hi Mark,

Thanks for your reply!

Sudip

On Mon, Feb 8, 2016 at 12:49 PM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> This is normal. Remember that vmd didn't read your topology file, it read a
> different .gro file each time and made different guesses about where bonds
> might be. See
> http://www.gromacs.org/Downloads/Related_Software/Visualization_Software
>
> Mark
>
> On Mon, Feb 8, 2016 at 6:58 AM Sudip Das <das.sudi...@gmail.com> wrote:
>
> > Dear users,
> >
> > I am simulating a system composed of protein,ionic liquid and water in
> > gromacs 5.0.2 (double precision). I am facing a problem listed below.
> >
> > 1.  trjconv_mpi_d -f trj.xtc -s run.tpr -o trj_unwrap.xtc -pbc mol
> >
> >  vmd trj_unwrap.xtc frame_before_run.gro
> >
> >  This is showing two unusual bonds.
> >
> > 2.  vmd trj_unwrap.xtc frame_after_run.gro
> >
> >  This is showing 10 unusual bonds, but here the residues, which are
> > forming before two unusualbonds, are not involved.
> >
> > 3. trjconv_mpi_d -f trj.xtc -s run.tpr -o trj_unwrap.gro -pbc mol
> >
> >  vmd trj_unwrap.gro
> >
> >  This is showing 10 unusual bonds, but here the residues, which are
> > forming before two unusualbonds, are not involved.
> >
> > 4. trjconv_mpi_d -f trj.xtc -s run.tpr -o trj_unwrap.pdb -pbc mol
> >
> >  vmd trj_unwrap.pdb
> >
> >  This is showing a large number of unusual bonds.
> >
> >
> >
> > Can anyone please sort out this problem?
> >
> > Thanks in advance,
> > Sudip
> > --
> > 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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> > send a mail to gmx-users-requ...@gromacs.org.
> >
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[gmx-users] unusual bonds

[Sudip Das]

Dear users,

I am simulating a system composed of protein,ionic liquid and water in
gromacs 5.0.2 (double precision). I am facing a problem listed below.

1.  trjconv_mpi_d -f trj.xtc -s run.tpr -o trj_unwrap.xtc -pbc mol

 vmd trj_unwrap.xtc frame_before_run.gro

 This is showing two unusual bonds.

2.  vmd trj_unwrap.xtc frame_after_run.gro

 This is showing 10 unusual bonds, but here the residues, which are
forming before two unusualbonds, are not involved.

3. trjconv_mpi_d -f trj.xtc -s run.tpr -o trj_unwrap.gro -pbc mol

 vmd trj_unwrap.gro

 This is showing 10 unusual bonds, but here the residues, which are
forming before two unusualbonds, are not involved.

4. trjconv_mpi_d -f trj.xtc -s run.tpr -o trj_unwrap.pdb -pbc mol

 vmd trj_unwrap.pdb

 This is showing a large number of unusual bonds.



Can anyone please sort out this problem?

Thanks in advance,
Sudip
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Re: [gmx-users] split MD trajectory into trajectories of smaller time duration

[Sudip Das]

Hi Swapnil,

You can use this command:

trjconv -s file.tpr -f file.xtc -o file_short_time.xtc -b t1 -e t2

where, t1= starting time
   t2= ending time

So, you can get the trajectory between time range t1 and t2 as your wish.

For detail, just type:

trjconv -h

Hope this will help you.

Regards,
Sudip

On Sat, Jan 16, 2016 at 8:16 PM, Swapnil Wagle 
wrote:

> Hi everyone..!
>
> I want to split an MD trajectory into smaller trajectories. Can someone
> please tell me how to do that?
> From the gromacs website I could find the solution only for splitting
> the trajectories of smaller subsystems, which is not what I want. I want
> the trajectories of the whole system for smaller time duration.
>
> Thanks,
> Swapnil
> --
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[gmx-users] RDF convergence

[Sudip Das]

Hi,

I am using g_rdf command (within gromacs-5.0.5) to calculate rdf as follow:

g_rdf_mpi_d -f .xtc -n .ndx -o rdf -cn

But the rdf is not getting converged to 1 exactly, rather it converges to
approximately 1.03. Whenever I am calculating rdf like this for different
sets of atoms, I am getting the same thing.

Can anyone please tell me why is this happening and what is the way out?
Any kind of help will be highly appreciated.

Thanks in advanced,

Sudip
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