Re: [gmx-users] calculation of self energy of protein

Thank you very much. On 27 March 2017 at 02:22, Justin Lemkul wrote: > > > On 3/26/17 4:49 PM, Saumyak Mukherjee wrote: > >> Dear Justin, >> >> Thanks for the reply. >> >> I have tried that already. I stripped out the protein trajectory using >> trjconv, created an appropriate

[gmx-users] MMPBSA analysis on GROMACS trajectory

Hi gromacs users, How to calculate MMPBSA analysis on Gromacs trajectory using MMPBSA tool of amber software package? Thanks, Neha -- 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

[gmx-users] Lipid water simulation

Hi all, I am trying to simulate 1024 dppc lipids with water. I have prepared my system using Charmm-Gui monolayer builder. Then I converted the atomistic system to coarse grained system using bacdward.py. The box size I got in the gro file was 18.246 18.38 23.7. Then I added CG water between

[gmx-users] Using the md integrator for calculating free energy of solvation

Hi, I am following Dr. Sander Pronk's and Dr. Justin Lemkul's tutorial on calculating free energy of solvation. Is it possible and theoretically sound to use the md integrator instead of the sd integrator for these calculations? I have already done a considerable amount of work using md

Re: [gmx-users] calculation of self energy of protein

On 3/26/17 4:49 PM, Saumyak Mukherjee wrote: Dear Justin, Thanks for the reply. I have tried that already. I stripped out the protein trajectory using trjconv, created an appropriate .tpr file using tpbconv (I am using GROMACS 4.5.6), and recalculated energy using mdrun -rerun. But does the

Re: [gmx-users] calculation of self energy of protein

Dear Justin, Thanks for the reply. I have tried that already. I stripped out the protein trajectory using trjconv, created an appropriate .tpr file using tpbconv (I am using GROMACS 4.5.6), and recalculated energy using mdrun -rerun. But does the resulting .edr file include only the inherent

Re: [gmx-users] Replica exchange: exchanging pressures

On 3/26/17 4:25 PM, Ramon Crehuet Simon wrote: Dear all, I'd like to run a replica exchange, but instead of exchanging temperatures, I would like to exchange pressures. I know this does not help enhance sampling, but I would like to create several ensembles at different pressures and I want

[gmx-users] Replica exchange: exchanging pressures

Dear all, I'd like to run a replica exchange, but instead of exchanging temperatures, I would like to exchange pressures. I know this does not help enhance sampling, but I would like to create several ensembles at different pressures and I want them to mix, as RE does. After preparing and

Re: [gmx-users] Protein preparation

On 3/26/17 12:39 PM, Quin K wrote: Thank you for the reply. I have another question. I used MODELLER on Chimera to fix the protein and found that there were significant visible changes to structure of protein. I'm not sure whether to use the old protein or the fixed one. Does it really matter

Re: [gmx-users] Protein preparation

Thank you for the reply. I have another question. I used MODELLER on Chimera to fix the protein and found that there were significant visible changes to structure of protein. I'm not sure whether to use the old protein or the fixed one. Does it really matter that I used unfixed protein if the

Re: [gmx-users] Clarification for the meaning of ncoords in GROMACS 5.0.4 pull code

Thank you very much. I really appreciate your help. On Sun, Mar 26, 2017 at 6:16 PM, Justin Lemkul wrote: > > > On 3/24/17 1:54 PM, Sajeewa Pemasinghe wrote: > >> Hi, >> >> I have two molecules which are not moving in the z axis due to being >> continuous across the periodic

Re: [gmx-users] Need for a clarification between "umbrella restraints" and value for "ncoords" in GROMACS pull code

Thank you very much. I really appreciate it. On Sun, Mar 26, 2017 at 6:17 PM, Justin Lemkul wrote: > > > On 3/26/17 8:11 AM, Sajeewa Pemasinghe wrote: > >> Hi all, >> >> I have a system in which I need to maintain the center of mass distance >> between two molecules constant

Re: [gmx-users] Secondary structure analysis

I think dssp is a useful tool for this purpose... Souparno On 26 Mar 2017 19:50, "Justin Lemkul" wrote: > > > On 3/26/17 8:21 AM, RAHUL SURESH wrote: > >> I use gromacs 2016.1 version. How to do secondary structure analysis ? >> >> >

Re: [gmx-users] calculation of self energy of protein

On 3/26/17 10:06 AM, Saumyak Mukherjee wrote: Yes, I need to calculate the inherent potential energy of the protein. You can strip the protein coordinates from the original trajectory, create a matching .tpr with convert-tpr and re-calculate energies with mdrun -rerun. The quantity is a

Re: [gmx-users] Protein preparation

On 3/26/17 9:44 AM, Quin K wrote: Hi I'm new to Gromacs. I have a question regarding protein preparation for MD simulation. I ran a 50 ns MD simulation but later found out that the protein has a charge. I found that there is a Mg2+ Ion in the protein crystal structure. Should I remove this

Re: [gmx-users] Secondary structure analysis

On 3/26/17 8:21 AM, RAHUL SURESH wrote: I use gromacs 2016.1 version. How to do secondary structure analysis ? http://manual.gromacs.org/documentation/2016.1/user-guide/cmdline.html#protein-specific-analysis -Justin -- == Justin A. Lemkul,

Re: [gmx-users] Gromacs for polymer and biomolecule system

On 3/26/17 8:46 AM, Riya Rogers wrote: Dear All I am new to Gromacs, I wanted to simulate Polymer system with biomolecule. Is there any tutorial? Also, how to include CNT with protein? Any suggestions ? In general, use pdb2gmx to generate the protein topology, then generate your

Re: [gmx-users] Need for a clarification between "umbrella restraints" and value for "ncoords" in GROMACS pull code

On 3/26/17 8:11 AM, Sajeewa Pemasinghe wrote: Hi all, I have a system in which I need to maintain the center of mass distance between two molecules constant for an umbrella window. The structures are not strictly aligned along an axis as they are the product of an equilibrium simulation.I

Re: [gmx-users] Clarification for the meaning of ncoords in GROMACS 5.0.4 pull code

On 3/24/17 1:54 PM, Sajeewa Pemasinghe wrote: Hi, I have two molecules which are not moving in the z axis due to being continuous across the periodic boxes. I want to keep the distance between them fixed by pulling along x and y axes. So as I am pulling along x and y axes does my ncoords = 2

Re: [gmx-users] Pull code grompp error

On 3/24/17 11:18 AM, Souparno Adhikary wrote: Hi Kausar, I tried it with an index file. It seemed to run fine but did not produce any "pull" i.e. shifting away of the DNA molecule from the protein. I used a harmonic potential. And also, why do I need to specify the index file when, according

Re: [gmx-users] Calculate area per head group

On 3/23/17 3:50 PM, Poncho Arvayo Zatarain wrote: Hello Gromacs users: I know there is not about Gromacs, but i want to calculate area per headgroup through simulation time. Anybody knos about a tutorial of GridMAT or can help me please? Thanks We give examples in the Appendix of the

Re: [gmx-users] gmx bar histogram data

On 3/23/17 3:16 PM, Eric Smoll wrote: Hello GROMACS users, I am using the "gmx bar" tool in GROMACS 5.1.2 and am interested in understanding the relevance of the histogram data output by the -oh flag. Dr. Lemkul provides a very helpful reference

Re: [gmx-users] Regarding Glycine structure

On 3/23/17 2:05 PM, Dilip H N wrote: Hello, I have a non zwitter ionic glycine molecule [NH2CH2COOH] in water, and in the first step if i do the energy minimization and then visualizes the mixture, the glycine is no more in its pure form as before instead it has been converted to its zwitter

Re: [gmx-users] GPU computing for explicit solvation systems

On 3/22/17 12:48 PM, mina solhtalab wrote: Hi,I'd like to know if it is possible to use GPU computing for running simulations in GROMACS (version 5.1.4) while using an "explicit solvation system". I saw in the GROMACS website that the first attempts in GPU computing for GROMACS was only

Re: [gmx-users] calculation of self energy of protein

Yes, I need to calculate the inherent potential energy of the protein. On 26 March 2017 at 14:33, Souparno Adhikary wrote: > Do you mean the potential energy of the protein? > > On 26 Mar 2017 14:24, "Saumyak Mukherjee" > wrote: > > > Dear

[gmx-users] Protein preparation

Hi I'm new to Gromacs. I have a question regarding protein preparation for MD simulation. I ran a 50 ns MD simulation but later found out that the protein has a charge. I found that there is a Mg2+ Ion in the protein crystal structure. Should I remove this Mg2+ ion from protein before addition

[gmx-users] Gromacs for polymer and biomolecule system

Dear All I am new to Gromacs, I wanted to simulate Polymer system with biomolecule. Is there any tutorial? Also, how to include CNT with protein? Any suggestions ? Regards Riya -- Gromacs Users mailing list * Please search the archive at

[gmx-users] Gromacs for polymer and biomolecule system

Dear All I am new to Gromacs, I wanted to simulate Polymer system with biomolecule. Is there any tutorial? Also, how to include CNT with protein? Any suggestions ? Regards Riya -- Gromacs Users mailing list * Please search the archive at

[gmx-users] Secondary structure analysis

I use gromacs 2016.1 version. How to do secondary structure analysis ? -- *Regards,* *Rahul Suresh* *Research Scholar* *Bharathiar University* *Coimbatore* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

[gmx-users] Need for a clarification between "umbrella restraints" and value for "ncoords" in GROMACS pull code

Hi all, I have a system in which I need to maintain the center of mass distance between two molecules constant for an umbrella window. The structures are not strictly aligned along an axis as they are the product of an equilibrium simulation.I have the following code. pull = umbrella

Re: [gmx-users] calculation of self energy of protein

Do you mean the potential energy of the protein? On 26 Mar 2017 14:24, "Saumyak Mukherjee" wrote: > Dear Users, > > How can the self energy of a protein be calculated from GROMACS. This means > that I want only the inherent energy of the protein, excluding the >

[gmx-users] calculation of self energy of protein

Dear Users, How can the self energy of a protein be calculated from GROMACS. This means that I want only the inherent energy of the protein, excluding the interaction energy with the surrounding solvent. Adding to this, is it possible to calculate such inherent energy of any selected domain in