Re: [gmx-users] hydrophobic interactions

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

Re: [gmx-users] Complementing the missing resideus of the protein

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

[gmx-users] Average pressure in CG simulation of oil-water system at NAPzT ensemble

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

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

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

Re: [gmx-users] Gromacs tabulated potentials for CG models

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

[gmx-users] Gromacs tabulated potentials for CG models

-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

[gmx-users] Two pair_styles for same atomtypes

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

Re: [gmx-users] Calculation of shape change of a protein during simulation

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

[gmx-users] Calculation of shape change of a protein during simulation

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

Re: [gmx-users] Related to REMD

312322335 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

Re: [gmx-users] Related to REMD

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

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

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

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

: 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

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

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

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

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

[gmx-users] Hydrophobic and hydrophilic SASA for a particular portion of a protein

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

[gmx-users] gmx sasa

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.

[gmx-users] gmx sasa

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.

Re: [gmx-users] RDF from NPT simulation?

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 6:3

[gmx-users] RDF from NPT simulation?

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 -- Gromacs Users mailing list * Please search the archive at

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

.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

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

"/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 carri

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

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

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

; > > > 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. > > > > > >

[gmx-users] CGMD simulation is not running with antifreeze water beads and 20 fs timestep

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

[gmx-users] Is dssp required with CG ElNeDyn model?

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

Re: [gmx-users] How to install g_fg2cg

ticular, 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

[gmx-users] How to install g_fg2cg

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.

Re: [gmx-users] Missing bond

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

[gmx-users] Missing bond

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

Re: [gmx-users] PLUMED Meeting 2017

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

Re: [gmx-users] PLUMED Meeting 2017

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

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

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

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

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 misunders

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

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: > &g

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

ned 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

[gmx-users] Wrong pressure with rigid water

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

[gmx-users] Fwd: Change in dihedral angle

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,

Re: [gmx-users] unusual bonds

here 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,io

[gmx-users] unusual bonds

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

Re: [gmx-users] split MD trajectory into trajectories of smaller time duration

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.

[gmx-users] RDF convergence

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