Re: [gmx-users] Kindly help

Dear Kalpana, As you would note in the output files, grompp throws one warning . The way warnings work in grompp is to not allow obviously inconsistent choices of options. So if there is warning(s) while running grompp, no .tpr file is generated. However, there may be some situations (as in your

Re: [gmx-users] Query regarding protein topology constructed using -vsite hydrogen option.

, 2018 at 7:43 PM Abhishek Acharya wrote: > Dear Gromacs Users, > > I am trying to simulate a protein ligand complex and since the system is > quite large, thought to use virtual sites implementation for all hydrogen > atoms. I have generated a topology for the protein chain using p

Re: [gmx-users] parallelizing gromacs2018.4

Hi. You can add the following line to the PBS script. export OMP_NUM_THREADS=4 -np should now become 5 in the mpirun command. Abhishek On Fri 23 Nov, 2018, 22:20 Mark Abraham, wrote: > Hi, > > Looks like nodes=1:ppn=20 sets the number of openmpi threads per rank to be > 20, on your cluster.

[gmx-users] Query regarding protein topology constructed using -vsite hydrogen option.

Dear Gromacs Users, I am trying to simulate a protein ligand complex and since the system is quite large, thought to use virtual sites implementation for all hydrogen atoms. I have generated a topology for the protein chain using pdb2gms -vsite hydrogen option. But, I notice that the protein

Re: [gmx-users] Large differences in calculated and experimental relative hydration free energy.

ocol work for > a simpler molecule? > > Mark > > On Fri, Aug 10, 2018, 13:33 Abhishek Acharya > wrote: > > > Dear Gromacs Users, > > > > I am trying to calculate the relative hydration free energy of Catechol > wrt > > Benzene as a way of validating the parameter

Re: [gmx-users] Protein-Ligand in bilayer

: > Thank you. > > I wanna know of the alternative method to carry out this simulation. other > than using charmm gui. > thank you > > On Fri, Aug 10, 2018 at 2:07 PM, Abhishek Acharya < > abhi117acha...@gmail.com> > wrote: > > > I see. I have not used

[gmx-users] Large differences in calculated and experimental relative hydration free energy.

(between experimental and calculated values) of the order of 1.5-2 kcal/mol as seen in case of hydration free energies of test cases used in the LigParGen paper. It would be nice to get some pointers as to what might be going wrong with my setup. Thanks in advance. Abhishek Acharya -- Gromacs Users

Re: [gmx-users] Protein-Ligand in bilayer

Hi. > > Thank you. > > But the system (protein ligand) is being constructed in charm gui input > generator, where it automatically compare the complex pdb and ligand mol2 > file ( which will Ben uploaded ). > > On Thu, 9 Aug 2018 at 11:24 PM, Abhishek Acharya > > wrote: >

Re: [gmx-users] Protein-Ligand in bilayer

Hi, > It look so complicated to carry out a protein ligand simulation in Lipid > bilayer system using charmm ff. I have a ligand with 27 atoms ( includes > Hydrogen ). The initial structure (monomer) is simulated in popc > constructed using charmm gui web page. To construct the same for the >

Re: [gmx-users] Calculation for number of ions

> Hi all, > > I want to run simulation of GPCR in POPC bilayer, but the GPCR N-terminal > is very flexible and negatively charged whereas the ICL's and C-terminal is > highly positively charged. Thus, the they interact with each other during > simulation. > Is there a reason to assume that they

Re: [gmx-users] REMD Showing Zero Exchange Probability

Hello, The REMD generator provides an estimate of the number of replicas that may be necessary (based on the system size) for performing replica exchange properly. Since you got 47 replicas, you can maybe play around with replicas more or less around that range. Maybe 16 replicas is much less for

Re: [gmx-users] Incorrect number of parameters in improper dihedral

Hello, In the OPLSAA ffbonded.itp, it is also mentioned that improper torsions for planar groups are implemented in gromacs as proper dihedrals. So, I think you are using the wrong function type here (type 2); you should use type 1 in this case. Hope this helps. Best, Abhishek On Tue, Jul 17,

Re: [gmx-users] Performing energy minimisation for an alanine scan

ity of Oxford > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Abhishek > Acharya > Sent: 09 July 2018 13:19:07 > To: Discussion list for GROMACS users > S

Re: [gmx-users] Performing energy minimisation for an alanine scan

. Abhishek Abhishek Acharya Research Associate, Department of Molecular Nutrition CSIR-Central Food Technological Research Institute, Mysuru-570020 On Mon, Jul 9, 2018 at 5:36 PM, Anthony Nash wrote: > Hello Abhishek, > > > I think you are onto something there. I've just found the mut

Re: [gmx-users] Performing energy minimisation for an alanine scan

possible aa to aa transformations. So, for alanine scanning, I would try to replace all [X2A] sections in mutres.mtp to just ala topology (X=any aa). Hope this helps. Abhishek Acharya On Mon, Jul 9, 2018 at 3:15 AM, Anthony Nash wrote: > Thanks Mark, sounds like a good idea. > > >

Re: [gmx-users] Error running mdrun (v-5.1.4) on a linux cluster.

, the same I had to use for compilations. Seems to me that PBS env variables were not set correctly within that session. When I submit the job outside of qlogin session, it works as expected. Thank again for pointing towards the right direction. Abhishek Acharya Research Associate, Department

[gmx-users] Error running mdrun (v-5.1.4) on a linux cluster.

Dear GROMACS users, I installed mpi-enabled GROMACS (mdrun only) on a linux cluster. The administrators recommended using Intel MPI so I used that. I also installed a local version of gcc-5.5.0 (with required dependencies), as the version available system-wide (4.4.6 I believe) was not compatible

Re: [gmx-users] Metal Ion Modelling

show to allow correct dynamics of the protein and also supports ligand exchange processes. But according to my knowledge, it hasn't been used much for studying protein dynamics as yet. You can try both the non-bonded and dummy model and see compare the results. Regards, Abhishek Acharya On Sat

Re: [gmx-users] Permeability determination

, but I think he means that in your case the movement of the membrane along the z-axis does not matter since the system is periodic; what matters is the relative movement of the ligand with respect to the membrane. I hope it is clear now. Regards, Abhishek Acharya Abhishek Acharya Research Associate

Re: [gmx-users] Free Energy Calculations: Error during minimization step.

. Sincerely, Abhishek Abhishek Acharya Research Associate, Department of Molecular Nutrition CSIR-Central Food Technological Research Institute, Mysuru-570020 On Tue, Sep 12, 2017 at 5:22 PM, Wes Barnett <w.barn...@columbia.edu> wrote: > On Tue, Sep 12, 2017 at 12:17 AM, Abhishe

Re: [gmx-users] Free Energy Calculations: Error during minimization step.

Thanks in advance. Abhishek Acharya Research Associate, Department of Molecular Nutrition CSIR-Central Food Technological Research Institute, Mysuru-570020 On Tue, Sep 12, 2017 at 9

Re: [gmx-users] Free Energy Calculations: Error during minimization step.

help will be greatly appreciated. Sincerely, Abhishek Abhishek Acharya Research Associate, Department of Molecular Nutrition CSIR-Central Food Technological Research Institute, Mysuru-570020 On Sun, Sep 10, 2017 at 8:02 AM, Abhishek Acharya <abhi117acha...@gmail.com> wrote: > > &g

Re: [gmx-users] Free Energy Calculations: Error during minimization step.

=none and c-lambda1 = vdw (or vice-versa). It doesn't matter if the topology files have the charges or not. Therefore, i had included the charges in my topology file. Then this explains the problem in my case. Thank you so much Wes for clarifying that out. Sincerely, Abhishek Acharya -- Gromacs Users

Re: [gmx-users] Free Energy Calculations: Error during minimization step.

ification will be very helpful. Sincerely, Abhishek Acharya -- 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 vi

[gmx-users] Free Energy Calculations: Error during minimization step.

and step10c.pdb did not reveal any obvious clashes between water molecules. I have also run simulations for charge annihilation step and I did not face such a problem. Looking for the some advice on how to proceed from here. Sincerely, Abhishek Acharya -- Gromacs Users mailing list * Please search

Re: [gmx-users] Creating metal ion dummy models for MD simulations.

and the details are all available in the article. I hope this info helps others in the user list. Sincerely, Abhishek Abhishek Acharya Research Associate, Department of Molecular Nutrition CSIR-Central Food Technological Research Institute, Mysuru-570020 On Tue, Jul 25, 2017 at 10:50 PM, Mark

[gmx-users] Creating metal ion dummy models for MD simulations.

to construct the coordinates for such dummy models ? Thanks and Regards, Sincerely, Abhishek Acharya Department of Molecular Nutrition CSIR-Central Food Technological Research Institute, Mysuru-570020 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support

Re: [gmx-users] Multiple output log. xtc .edr files generated using mpirun

Thanks Mark for your reply. In that case, it is confirmed that the problem is with the installation. I will try to get the package reinstalled. Thanks again. Best Regards, -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List

Re: [gmx-users] Multiple output log. xtc .edr files generated using mpirun

Thanks Nikhil, for your response. But could I get a little more clue as to what mistake you are alluding to? I have again checked the link but I don't seem to find the mistake with the command. Thanks and Regards. Abhishek Acharya Research Associate, Department of Molecular Nutrition CSIR

[gmx-users] Multiple output log. xtc .edr files generated using mpirun

understand where the problem seems to be. Thanks in advance. Sincerely, Abhishek Acharya Research Associate, Department of Molecular Nutrition CSIR-Central Food Technological Research Institute, Mysuru-570020 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org

Re: [gmx-users] Unexpected behavior in the output of gmx insert-molecules using the -ip option.

a > coordinates, but it becomes an effort if a large number of systems need to > be > generated. > > Thank you. > > Regards, > Abhishek Acharya > Research Associate, > Department of Molecular Nutrition > CSIR-Central Food Technological Research Institute, >

[gmx-users] Unexpected behavior in the output of gmx insert-molecules using the -ip option.

stems need to be generated. Thank you. Regards, Abhishek Acharya Research Associate, Department of Molecular Nutrition CSIR-Central Food Technological Research Institute, Mysuru-570020 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_L

Re: [gmx-users] g_rms using a structure in trajectory as reference

the rmsf analysis on the equilibrated segment alone. Regards, Abhishek Acharya On May 29, 2017 18:26, "Francesca Lønstad Bleken" < francesca.l.ble...@sintef.no> wrote: > Hi, > > I am trying to understand how to best use a chose frame in the trajectory > as referenc

Re: [gmx-users] Unexpected behavior in the output of gmx insert-molecules using the -ip option.

Sorry, I forgot to mention one important detail. I am using gromacs version 2016. I tried gromacs 5.1.2 also; it shows the same behavior. Regards, Abhishek Acharya Research Associate, Department of Molecular Nutrition CSIR-Central Food Technological Research Institute, Mysuru-570020 On Mon

[gmx-users] Unexpected behavior in the output of gmx insert-molecules using the -ip option.

stems need to be generated. Thank you. Regards, Abhishek Acharya Research Associate, Department of Molecular Nutrition CSIR-Central Food Technological Research Institute, Mysuru-570020 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_L

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

with 4.6.5 you gromacs has used a group cut-off scheme, whereas 5.0 has used verlet scheme. For system with water molecules, group scheme gives better performance than verlet. For more check out: http://www.gromacs.org/Documentation/Cut-off_schemes Regards, Abhishek Acharya On Fri, Sep 5, 2014 at 7

[gmx-users] Performance of beowulf cluster

specs for a 100,000 atom simulation box ? Also, is it better to invest in a single 48 core server ? The cluster system can be set up at almost half the price of a 48 core server, but do we lose out on performance in the process?? Regards, Abhishek Acharya -- Gromacs Users mailing list