Re: [gmx-users] PBC issues with membrane-peptide simulation

a branched antimicrobial peptide perturbs a bacterial membrane and enhances permeability. Biochim. Biophys. Acta *1828*, 1112–1121. Best Regards, Abhishek Acharya On Thu, Nov 10, 2016 at 12:48 PM, Abhi Acharya <abhi117acha...@gmail.com> wrote: > Sorry for that Mark. > >

Re: [gmx-users] PBC issues with membrane-peptide simulation

<mark.j.abra...@gmail.com> wrote: > Hi, > > You haven't said what you're trying to model, so it's going to be hard for > someone to help out :-) > > Mark > > On Thu, 10 Nov 2016 05:21 Abhi Acharya <abhi117acha...@gmail.com> wrote: > > > Thank you Stephane for y

Re: [gmx-users] PBC issues with membrane-peptide simulation

To resolve your problem you could simulate two > bilayer in box and insert the peptides between them. > > HTH > > -- > > Message: 6 > Date: Wed, 9 Nov 2016 16:07:26 +0530 > From: Abhi Acharya <abhi117acha...@gmail.com> > To: gromacs.org_

[gmx-users] Fwd: PBC issues with membrane-peptide simulation

Dear Gromacs users, I am trying to simulate a system consisting of a lipid bilayer and few peptides. The peptides have been added randomly to the simulation box only on one side of the membrane. I ran a 100 ns simulation of the system using CHARMM36 forcefeild. However, I find that within the

Re: [gmx-users] Center-of-Mass motion removal setting for Membrane system with multiple peptides.

system as one group for COM > removal is appropriate. The lipid diffusion may not be 100% correct, but > depending on the aims of the study it may not be a significant factor. > > -Justin > > Kind regards, >> Erik >> >> On 28 Sep 2016, at 16:39, Abhi Acharya <abhi117

Re: [gmx-users] Center-of-Mass motion removal setting for Membrane system with multiple peptides.

Thank you Eric for your clarification. However, I have seen that in membrane simulations, its is suggested to couple membrane, and solvent and solute to two different COM groups. The argument is that in case of membrane systems, there is an inherent tendency of lateral drift of membranes; with a

Re: [gmx-users] Center-of-Mass motion removal setting for Membrane system with multiple peptides.

concern in your > case? > > Erik > > > On 27 Sep 2016, at 10:40, Abhi Acharya <abhi117acha...@gmail.com> wrote: > > > > Another thing which I don't understand is in case of the peptide group, > > which I expect to diffuse freely, would COM motion removal b

Re: [gmx-users] Center-of-Mass motion removal setting for Membrane system with multiple peptides.

would assume that translational, rotational and conformational freedom would be required. Wouldn't restricting the COM restrict its dof? Thanks. On Tue, Sep 27, 2016 at 1:59 PM, Abhi Acharya <abhi117acha...@gmail.com> wrote: > What I meant to ask was a way to ensure that the peptides and

Re: [gmx-users] Center-of-Mass motion removal setting for Membrane system with multiple peptides.

such as this. Just wanted to be sure, before I start the production runs. On Tue, Sep 27, 2016 at 1:01 PM, Erik Marklund <erik.markl...@kemi.uu.se> wrote: > > > On 27 Sep 2016, at 06:26, Abhi Acharya <abhi117acha...@gmail.com> wrote: > > > > Dear Gromacs user

[gmx-users] Center-of-Mass motion removal setting for Membrane system with multiple peptides.

Dear Gromacs users, I am trying to perform a simulations of different concentration of peptides in a box with lipid bilayer. In this context, I had a query regarding the correct Center-of-Mass removal settings; what would be the correct way to ensure that the Membrane is stationary during long

Re: [gmx-users] trjconv: choosing name for a large number of output gro files

Hello, You can use the -sep flag with trjconv command ave your output files serially numbered from 0. Regards Abhishek On Wed, Apr 29, 2015 at 10:12 PM, Athina Meletiou enxa...@nottingham.ac.uk wrote: Dear Gromacs users, I want to use trjconv to extract frames from a long simulation in

[gmx-users] Error in generated Replica Exchange statistics in log file

Hello GROMACS users, I have a problem with the Replica Exchange statistics printed in log file. I ran a 25 ns Replica exchange on a cluster through a queuing system. However, due to insufficient wall time the job stopped abruptly around 24 ns and no stats were printed in the log file. I then

[gmx-users] Regarding g_cluster output.

Hello Gromacs users. I ran g_clustsize on a trajectory file. The output gives the cluster members in the last column. I don't understand, how these members are numbered. My trajectory contains 25001 frames whereas the members are numbered till 5. The output I get is as follows: Using gromos

Re: [gmx-users] Using COM pulling and Enforced Rotations together

Abhishek Acharya Shasara Research Foundation On Tue, Jan 6, 2015 at 3:57 PM, Carsten Kutzner ckut...@gwdg.de wrote: Hi Abhishek Acharya, On 06 Jan 2015, at 11:06, Abhi Acharya abhi117acha...@gmail.com wrote: Hello Gromacs users, I would like to use COM pulling and Enforced rotations

[gmx-users] Using COM pulling and Enforced Rotations together

Hello Gromacs users, I would like to use COM pulling and Enforced rotations simultaneously on a single domain. Is it possible at all to do so? I tried to run an simulation; it ran fine without errors, but analysis indicates COM pulling may not have worked properly although the domain was rotated

Re: [gmx-users] Obtaining PMF for change in domain position

the pot. is evaluated rot_potfit_nsteps0 = 21 ; For fit type 'potential', distance in degrees between two consecutive angles rot_potfit_step0 = 0.25 Thanks in advance. Abhishek Acharya Shasara Research Foundation On Tue, Dec 30, 2014 at 5:15 PM, Abhi Acharya abhi117acha...@gmail.com

Re: [gmx-users] Obtaining PMF for change in domain position

Abhishek Acharya Shasara Research Foundation On Tue, Dec 30, 2014 at 10:42 AM, Justin Lemkul jalem...@vt.edu wrote: On 12/29/14 11:34 AM, Abhi Acharya wrote: On Mon, Dec 29, 2014 at 8:59 PM, Justin Lemkul jalem...@vt.edu wrote: On 12/29/14 6:57 AM, Abhi Acharya wrote: Hello GROMACS

[gmx-users] Obtaining PMF for change in domain position

Hello GROMACS Users, This is a problem I am facing for the first time. Kindly guide be to the best options. I have a protein which has two large domains connected by a flexible linker peptide (~10 aa). The two domains seem to interact with each other and have been crystallized in three different

Re: [gmx-users] Obtaining PMF for change in domain position

On Mon, Dec 29, 2014 at 8:59 PM, Justin Lemkul jalem...@vt.edu wrote: On 12/29/14 6:57 AM, Abhi Acharya wrote: Hello GROMACS Users, This is a problem I am facing for the first time. Kindly guide be to the best options. I have a protein which has two large domains connected by a flexible

Re: [gmx-users] s-s bond recognition

Hello. I would suggest you to first try energy minimization on the protein alone and see whether it solves the issue. If not, then try MD (without any S-S bonds) with distance restraints on the sulfur atoms of the particular Cys residues. See if that resolves the issue. Regards, Abhishek On Sun,

Re: [gmx-users] MD workstation for Gromacs

Hi, We use systems with 780 Ti , 12 cores and have had no problems running Gromacs. Gives a performance of ~ 100 ns/day for a system with 35000 atoms. Regards, Abhishek On Mon, Oct 27, 2014 at 7:05 PM, Adelman, Joshua Lev jl...@pitt.edu wrote: On Oct 27, 2014, at 3:14 AM, Carsten Kutzner

[gmx-users] Non-integer charges when using scaled-topology files for REST2 simulation.

Dear Gromacs users. While creating the .tpr files for a hamiltonian replex, I noticed that the grompp gives a note regarding Non-integer charges in case of the replicas with scaled potentials. I do not get such a note in case of the unscaled replica. My concern is that the charge values are

Re: [gmx-users] Non-integer charges when using scaled-topology files for REST2 simulation.

Hello, Thank you for replying. I have also come across a note on this issue in the following link: https://github.com/GiovanniBussi/plumed2/blob/v2.0-hrex/user-doc/tutorials/hrex.txt It says that Gromacs takes care of this by adding a compensating background, though I am not sure how exactly

Re: [gmx-users] Non-integer charges when using scaled-topology files for REST2 simulation.

now I will. Scott Using a compensating background charge is non-physical and can lead to artifacts. I personally would suggest to reject papers using it. On Tue, Oct 7, 2014 at 5:10 AM, Abhi Acharya abhi117acha...@gmail.com wrote: Hello, Thank you for replying. I have also come

[gmx-users] Limitation on the maximum number of OpenMPI threads

Hello, I was trying to run a simulation on Gromacs-4.6.3 which has been compiled without thread MPI on a BlueGene/Q system. The configurations per node are as follows: PowerPC A2, 64-bit, 1.6 GHz, 16 cores SMP, 4 threads per core For running on 8 nodes I tried: srun mdrun_mpi -ntomp 64 But,

Re: [gmx-users] Gromacs 5.0 compilation slower than 4.6.5. What wentwrong ?

-perform the Verlet scheme (depending whether you value buffering in the neighbour list, which you generally should!). Mark On Fri, Sep 5, 2014 at 4:06 PM, Abhi Acharya abhi117acha...@gmail.com wrote: Hello, Is you system solvated with water molecules? The reason I ask

Re: [gmx-users] Gromacs 5.0 compilation slower than 4.6.5. What went wrong ?

Hello, From the log files it is clear that out of 48 cores, the 5.0 run had 8 cores allocated to PME while the 4.6.5 run had 12 cores. This seems to have caused a greater load imbalance in case of the 5.0 run. If you notice the last table in both .mdp files, you will notice that the PME

Re: [gmx-users] Gromacs 5.0 compilation slower than 4.6.5. What went wrong ?

of PME ranks or decrease the cut-off and the grid spacing. I don't know much about Gromacs so I am puzzled. 2014-09-05 14:32 GMT+02:00 Abhi Acharya abhi117acha...@gmail.com: Hello, From the log files it is clear that out of 48 cores, the 5.0 run had 8 cores allocated

Re: [gmx-users] Performance of beowulf cluster

. Regards, Abhishek On Tue, Aug 12, 2014 at 6:00 AM, Szilárd Páll pall.szil...@gmail.com wrote: On Tue, Aug 5, 2014 at 5:21 PM, Abhi Acharya abhi117acha...@gmail.com wrote: Thank you Mirco and Szilard, With regards to the GPU system, I have decided on a Xeon E5-1650 v2 system with GEForce

Re: [gmx-users] Performance of beowulf cluster

Thank you Mirco and Szilard, With regards to the GPU system, I have decided on a Xeon E5-1650 v2 system with GEForce GTX -780 Ti GPU for equilibration and production runs with small systems. But for large systems or REMD simulations, I am a bit skeptical on banking on GPU systems. Any pointers as