[gmx-users] REMD analysis of trajectories

Hi, I have run a 100ns-REMD of protein, which has 20 replicas (i.e. remd1.xtc, remd2.xtc, ..., remd20.xtc). I want to analyze a trajectory at specific temperature such as a trajectory at experiment temperature 298K rather than analyzing the continuous trajectory. I have known GROMACS

Re: [gmx-users] System volume "jumps" on exact continuations

On Wed, May 31, 2017 at 9:44 PM, Christopher Neale < chris.ne...@alum.utoronto.ca> wrote: > 1. Once you identify a continuation (with associated run script) that > gives the discontinuity, if you run many repeats of the original > continuation then does the jump always occur or only sometimes? >

Re: [gmx-users] System volume "jumps" on exact continuations

1. Once you identify a continuation (with associated run script) that gives the discontinuity, if you run many repeats of the original continuation then does the jump always occur or only sometimes? 2. Did you do any of the MPI runs with -notunepme ? That would be my first suspect. 3. Did

[gmx-users] AMBER LIPID14 ff in GROMACS

Is there any way to use Amber Lipid14 force field parameters for GROMACS -- सस्नेह / with regards अमित सिंह / Amit Singh कम्प्यूटेशनल विज्ञान केंद्र / Centre for Computational Sciences बुनियादी और अनुप्रयुक्त विज्ञान स्कूल / School of Basic and Applied Sciences पंजाब केन्द्रीय विश्वविद्यालय /

Re: [gmx-users] Lipid Simulation Analysis

Hello, First of all you can try to reproduce basic lipid properties as the area per lipid and bilayer thickness. Both can be easily calculated from the position of lipid headgroups. Other useful properties is the diffusion rate of lipids (accessable by calculating the mean square displacement)

Re: [gmx-users] Deuterium Order Parameter Calculations

Thank you Justin, That makes much more sense. I was able to fix the error. I have one more question that is out of topic from the original question. Is there a guide that informs the user on what index groups should be made for each type of analysis? I am also trying to use gmx_potential to do

[gmx-users] System volume "jumps" on exact continuations

Dear GMX-USERS, We are observing abrupt, discontinuous “jumps” in our simulation box volume for different chunks of trajectory when performing exact continuations of standard, explicit solvent, MD simulations in the NPT ensemble. Note that these volume jumps do not appear to occur after every

Re: [gmx-users] Doubt about gmx wham analysis

Dear Justin, During the pulling part of the umbrella sampling for finding binding affinity of the Protien-ligand system, the ligand(peptide) is deformed and its helices straighten along with large conformational changes in Protein. This is when the pull_coord1_dim = Y Y Y. But when I had used

Re: [gmx-users] calculation of energy of individual water molecules in gromacs

Thanks a lot for your comments. I am doing the calculations using a self-written FORTRAN code. On 31 May 2017 at 17:23, Justin Lemkul wrote: > > > On 5/31/17 12:24 AM, Saumyak Mukherjee wrote: > >> Thanks Justin for the reply. >> >> Supposing that I have 2300 (average) water

Re: [gmx-users] Doubt about gmx wham analysis

Dear Justin, Many Thanks for the swift reply and the help in answering my doubts. Best Regards, Bhagyesh - Original Message - From: "Justin Lemkul" To: gmx-us...@gromacs.org Sent: Wednesday, May 31, 2017 6:06:59 PM Subject: Re: [gmx-users] Doubt about gmx wham

Re: [gmx-users] Doubt about gmx wham analysis

On 5/31/17 8:34 AM, Varvdekar Bhagyesh Rajendra wrote: Dear Justin, In my Protein-ligand system, I have used pull_coord1_dim = Y Y Y and the ligand is pulled along the COM of two groups protein-ligand in all directions to calculate binding affinity using umbrella sampling. On the other

Re: [gmx-users] Doubt about gmx wham analysis

Dear Justin, In my Protein-ligand system, I have used pull_coord1_dim = Y Y Y and the ligand is pulled along the COM of two groups protein-ligand in all directions to calculate binding affinity using umbrella sampling. On the other hand, the tutorials use pull_coord1_dim = N N Y. Hence, I

Re: [gmx-users] Reg: creation of separate chains in .pdb file

On 5/31/17 8:26 AM, Syed Azeem wrote: On 5/29/17 8:00 AM, Syed Azeem wrote: Hey all, I simulated a protein-peptide docked complex. Post simulation, I created an index file selecting only the Protein Group (protein-peptide complex). Then using editconf, I created a .pdb file for the same.

Re: [gmx-users] Reg: creation of separate chains in .pdb file

> On 5/29/17 8:00 AM, Syed Azeem wrote: >> Hey all, >> >> I simulated a protein-peptide docked complex. Post simulation, I >> created an index file selecting only the Protein Group >> (protein-peptide complex). Then using editconf, I created a .pdb file >> for the same. >> >> When I view the

[gmx-users] Simulated annealing

Hi all, I am using Gromacs version 4.5.6 for peptide simulation. The structure of the peptide (16mer) was predicted from Pepfold3 server. I did Simulated annealing so that the side chains get properly oriented and the predicted structure will reach its global optimum so that the structure

Re: [gmx-users] Atom type CB ERROR

On 5/31/17 1:18 AM, Kashif wrote: I got parameter file (ligand.par) from swissparam. What should I add from this file and where? means the topol.top file created during the simulation, should I use that file to include CB parameter? Please find the parameter data generated from swiss para and

Re: [gmx-users] Need to confirm parameters.

On 5/31/17 2:26 AM, Sailesh Bataju wrote: Extract the coordinates of any valine side chain in a protein, make an IBUT .hdb entry based off of it (all you'll need to do is change 2 -> 3 in the number of H added to the CB atom) and submit to pdb2gmx; it will build any missing H atoms for you.

Re: [gmx-users] How to perform final MD simulation after extending a NPT simulation

On 5/30/17 8:50 PM, Adarsh V. K. wrote: Dear all, *I used following command to extend a NPT simulation* gmx convert-tpr -s npt.tpr -extend 500 -o tpxout.tpr gmx mdrun -deffnm tpxout -cpi npt_prev.cpt -v *Now to do final MD simulation what command I should use?* gmx grompp -f md.mdp -c

Re: [gmx-users] calculation of energy of individual water molecules in gromacs

On 5/31/17 12:24 AM, Saumyak Mukherjee wrote: Thanks Justin for the reply. Supposing that I have 2300 (average) water molecules in a 1 nm hydration shell around a protein, I need to calculate the interaction energy of each and everyone of them in all the time frames, with the rest of the

Re: [gmx-users] DrudeFF topology transfer from CHARMM to GROMACS

On 5/31/17 7:06 AM, Tomasz Piskorz wrote: Dear all, I would like to simulate cyclohexane using Drude FF in GROMACS. I've seen that the topology is already available in CHARMM-DrudeFF and I would like to transfer it to GROMACS. However, I don't know how to calculate the charge of Drude

[gmx-users] Doubt about constrained NM

Dear all, Is it possible to do constrained Normal Mode Analysis in Gromacs such as a free ligand buried in a constrained protein to study the effects of the binding on the normal modes of ligand? I had tried to used DPOSRES_A, as my protein is chain A, but everytime gromacs throws the error

Re: [gmx-users] Lipid Simulation Analysis

Hi, What kind of information do you want to find? There are numbers of stuff you can do. -- 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 *

[gmx-users] DrudeFF topology transfer from CHARMM to GROMACS

Dear all, I would like to simulate cyclohexane using Drude FF in GROMACS. I've seen that the topology is already available in CHARMM-DrudeFF and I would like to transfer it to GROMACS. However, I don't know how to calculate the charge of Drude particle, which is required by topology in GROMACS.

[gmx-users] Positive potential energy

Hi allI run two simulations on a 16 aa peptide under the same conditions (forcefield, simulation duration, ...) except the solvent in one of the  simulations was TFE instead of water. The potential energy in the TFE containing system was positive (about 14 Kj/mol), while in water containing

[gmx-users] Positive potential energy

Hi allI run two simulations on a 16 aa peptide under the same conditions (forcefield, simulation duration, ...) except the solvent in one of the  simulations was TFE instead of water. The potential energy in the TFE containing system was positive (about 14 Kj/mol), while in water containing

[gmx-users] Lipid Simulation Analysis

Hello What kind of analysis can we perform for a lipid bilayer simulation? And which are the tools available in gromacs to analyse bilayer simulation? Thank You Regards Z. Hazarika Research Scholar Tezpur University Tezpur ___ D I S C L A I M E R This e-mail may contain

Re: [gmx-users] Doubt about gmx wham analysis

On Tue, May 30, 2017 at 4:19 PM, Varvdekar Bhagyesh Rajendra < bhagyesh.varvde...@research.iiit.ac.in> wrote: > Dear all, > > I have followed the Umbrella sampling tutorial ( > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ > gmx-tutorials/umbrella/index.html) on a Protein-ligand

Re: [gmx-users] Need to confirm parameters.

>Extract the coordinates of any valine side chain in a protein, make an IBUT >.hdb >entry based off of it (all you'll need to do is change 2 -> 3 in the number of >H >added to the CB atom) and submit to pdb2gmx; it will build any missing H atoms >for you. >-Justin I did exactly you said and