Re: [gmx-users] Insertion protein in the membrane via G_membed

On 20/06/2012 4:39 PM, James Starlight wrote: by the way I've forced with problems during insertion of the complex protein_ligand into membrane by means of g_membed firstly I've created index.ndx file with the merged protein_ligand group. Than I've used next mdp for my g_membed input integra

Re: [gmx-users] Insertion protein in the membrane via G_membed

by the way I've forced with problems during insertion of the complex protein_ligand into membrane by means of g_membed firstly I've created index.ndx file with the merged protein_ligand group. Than I've used next mdp for my g_membed input integrator = md energygrps = Protein ADN freezegr

[gmx-users] OPLS parametrs for aminoxide

Hi all, I would like to know if the force field parameters (OPLS) exist for the amine oxide group (for eg as in trimethyl amine oxide (CH3)3-N-O ). In the OPLS parameter file in the gromacs tp directory, I could find only paramters for the nitro group (NO2) and NO3- ion. MD simulation of dimethyld

[gmx-users] Re: Regarding pdb file of a polymer

Hi Justin Thank you for the reply. I have got my answer and its clear now. Regards Sreeta On 19 June 2012 16:55, Justin A. Lemkul [via GROMACS] < ml-node+s5086n4998714...@n6.nabble.com> wrote: > > > On 6/19/12 4:49 PM, sreeta.g wrote: > > Hi Justin > > Thank you for the reply. However, PRODRG is u

Re: [gmx-users] Re: Regarding pdb file of a polymer

On 6/19/12 4:49 PM, sreeta.g wrote: Hi Justin Thank you for the reply. However, PRODRG is used to generate topologies from simple pdb files. I am clear on how to create the pdb files for Well, it can also provide a simple way to generate coordinate files. It's a bit less convenient now that

[gmx-users] Re: Regarding pdb file of a polymer

Hi Justin Thank you for the reply. However, PRODRG is used to generate topologies from simple pdb files. I am clear on how to create the pdb files for polymers in general (The entire long chain, with as many molecules as required, using MS modelling.) My question, however is about how to arrive at

Re: [gmx-users] Regarding pdb file of a polymer

On 6/19/12 3:17 PM, sreeta.g wrote: Hi I am working with Polyvinyl Alcohol polymer. I have been following http://lists.gromacs.org/pipermail/gmx-users/2009-March/040125.html (procedure by Justin) this thread for a lot of guidance. I have obtained the coordinate file for PVA from other sources,

[gmx-users] Regarding pdb file of a polymer

Hi I am working with Polyvinyl Alcohol polymer. I have been following http://lists.gromacs.org/pipermail/gmx-users/2009-March/040125.html (procedure by Justin) this thread for a lot of guidance. I have obtained the coordinate file for PVA from other sources, however, I am unable to understand how

[gmx-users] email id for posting

sreeta...@gmail.com -- Sreeta Gorripaty -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. U

Re: [gmx-users] to know about constraints

On 6/19/12 2:35 PM, Anik Sen wrote: Hello Justin, This is Anik again. I checked the links. But could not understand fully. Am giving the part of the topology file as given below, generated with the command "pdb2gmx -f a.pdb -o b.pdb -p topol.top" The topology file :

Re: [gmx-users] pair interaction energy decomposition analysis

On 6/19/12 8:02 AM, Ngo Son Tung wrote: Dear Gromacs Users, I need calculate pair interaction energy decomposition analysis between Aromatic hydrocarbon ring and protein to discovery distribution of aromactic hydrocarbon ring of drug candidate in the interaction of ligand and protein. However,

RE: [gmx-users] to know about constraints

Hello Justin, This is Anik again. I checked the links. But could not understand fully. Am giving the part of the topology file as given below, generated with the command "pdb2gmx -f a.pdb -o b.pdb -p topol.top" The topology file : " 205CL-205CL- Cl

[gmx-users] Re: pair interaction energy decomposition analysis

you could check your .ndx file and make sure the atoms 389 and 391 are listed under the same group (i.e. protein ROU) Alternately, you could try using energygrps= System Please make sure that the value for energygrps is one of the groups listed in the .ndx file Shounak -- View this message in con

RE: [gmx-users] to know about constraints

Thanx Justin. I will check the links.. From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Tuesday, June 19, 2012 11:06 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users]

Re: [gmx-users] to know about constraints

On 6/19/12 1:28 PM, Anik Sen wrote: Dear gromacs developers, This is Anik. For a certain work with nonbonded interactions with alkali halides and water, I need to constrain some specific atoms in the energy minimization step. Is there any option to constra

[gmx-users] to know about constraints

Dear gromacs developers, This is Anik. For a certain work with nonbonded interactions with alkali halides and water, I need to constrain some specific atoms in the energy minimization step. Is there any option to constrain the atoms in a specific calculati

[gmx-users] How do you properly use g_msd to calculate MSD of bilayer and account for monolayer motion?

Hello, I simulated a pure DPPC bilayer at 323 K under semi-isotropic conditions and have a somewhat small area per lipid of .615 nm^2. I also wrote my own code to calculate the average Mean Square Displacement and Diffusion Coefficient of the lipids, taking into account the relative motions of the

[gmx-users] CMAP and Free Energy

Dear gromacs developers, is there any plan to make the CMAP correction avalaible for Free Energy Calculations? Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/

Re: [gmx-users] CMAP in Gromacs Vs. CHARMM

On 20/06/2012 12:19 AM, Andy Somogyi wrote: Hi, I'm trying to figure out the differences between Gromacs and CHARMM implementation of CMAP. In Gromacs it seems to be defined as a 5 body term, whereas in CHARMM, its a 8 body term. I thought CMAP was a correction between a pair of dihedrals, 4

[gmx-users] CMAP in Gromacs Vs. CHARMM

Hi, I'm trying to figure out the differences between Gromacs and CHARMM implementation of CMAP. In Gromacs it seems to be defined as a 5 body term, whereas in CHARMM, its a 8 body term. I thought CMAP was a correction between a pair of dihedrals, 4 atoms define a dihedral, so I'm not sure h

Re: [gmx-users] error in g_cluster "diagonalization" method

On 20/06/2012 12:03 AM, Isaure Chauvot de Beauchêne wrote: Hi, I'm trying to cluster 200 structure of a 20 aas peptide, by the g_cluster "diagonalization" method. There is my command line: * g_cluster -f all_1-200.pdb -s ../pdb/FinalGSAFold_1.pdb -clid -cl clusters.pdb -m

[gmx-users] error in g_cluster "diagonalization" method

Hi, I'm trying to cluster 200 structure of a 20 aas peptide, by the g_cluster "diagonalization" method. There is my command line: * g_cluster -f all_1-200.pdb -s ../pdb/FinalGSAFold_1.pdb -clid -cl clusters.pdb -method diagonalization -o rmsd-clust.xpm -g cluster.log **

Re: Fw: [gmx-users] segmentation fault-g_spatial

On 6/19/12 9:34 AM, delara aghaie wrote: - Forwarded Message - *From:* delara aghaie *To:* Discussion list for GROMACS users *Sent:* Tuesday, 19 June 2012, 12:04 *Subject:* [gmx-users] segmentation fault-g_spatial Dear Gromacs users. I have a protein in a box of water. I want to cal

Fw: [gmx-users] segmentation fault-g_spatial

- Forwarded Message - From: delara aghaie To: Discussion list for GROMACS users Sent: Tuesday, 19 June 2012, 12:04 Subject: [gmx-users] segmentation fault-g_spatial Dear Gromacs users. I have a protein in a box of water. I want to calculate the SDF of water molecules around the

Re: [gmx-users] Analysis of the torsion Chi angles dynamics during simulation

On 6/19/12 9:24 AM, James Starlight wrote: Dear Gromacs Users! I want to perform analysis of the chosen Chi1 angles during md simulation. How I could obtain such graphs with the dependence of the dynamics ( distribution in degrees) of that torsions on the simulation time ? g_angle can ana

[gmx-users] Analysis of the torsion Chi angles dynamics during simulation

Dear Gromacs Users! I want to perform analysis of the chosen Chi1 angles during md simulation. How I could obtain such graphs with the dependence of the dynamics ( distribution in degrees) of that torsions on the simulation time ? Thanks for help James -- gmx-users mailing listgmx-users

Re: [gmx-users] (no subject)

On 6/19/12 8:58 AM, ankita oindrila wrote: I am doing simulation of membrane protein in lipid bilayer for my college project!. After making the complex of protein and lipid bilayer, I was going to the step using genbox to solvate the system. The error that i am now getting is : Fat

[gmx-users] (no subject)

I am doing simulation of membrane protein in lipid bilayer for my college project!. After making the complex of protein and lipid bilayer, I was going to the step using genbox to solvate the system. The error that i am now getting is : Fatal error: Not enough memory. Failed to realloc 10

[gmx-users] pair interaction energy decomposition analysis

Dear Gromacs Users, I need calculate pair interaction energy decomposition analysis between Aromatic hydrocarbon ring and protein to discovery distribution of aromactic hydrocarbon ring of drug candidate in the interaction of ligand and protein. However, when I try to run MD with zero step from t

Re: [gmx-users] REMD in explicit solvent

On 19/06/2012 5:55 PM, Esben Jannik Bjerrum wrote: Hi Gromacs Users I'm new to list, but hope to get a little help from someone experienced with setting up some replica exhange simulations in explicit solvent. It keeps exploding after app. 50 to 200 ps simulation time. It runs fine up to

Re: [gmx-users] Trjconv error

Actually, I loaded the trajectory of md-run and saw the bonds stretching and behaves strangely . So, as Justin suggested, I decided to do as the work-flow of PBC. So I entered the commands as below:  1.  First make your molecules whole if you want them whole     trjconv -f md.trr -s md.

Re: [gmx-users] Trjconv error

On 19/06/2012 5:49 PM, Shima Arasteh wrote: Thanks for your reply. I entered the trjconv as the workflow of http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions And I chose the 'system' as the chosen group. Now, if I want to see the trajectory, am I supposed to load

[gmx-users] REMD in explicit solvent

Hi Gromacs Users I'm new to list, but hope to get a little help from someone experienced with setting up some replica exhange simulations in explicit solvent. It keeps exploding after app. 50 to 200 ps simulation time. It runs fine up to there, and then suddently one or a couple of atoms ge

Re: [gmx-users] Trjconv error

Thanks for your reply. I entered the trjconv as the workflow of  http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions And I chose the 'system' as the chosen group. Now, if I want to see the trajectory, am I supposed to load the mdfinal.xtc on the first frame ( 1stfram

[gmx-users] segmentation fault-g_spatial

Dear Gromacs users. I have a protein in a box of water. I want to calculate the SDF of water molecules around the protein. I have used the procedure described in this page: http://www.gromacs.org/Documentation/Gromacs_Utilities/g_spatial after two times using trjconv for putting the protein in

RE: [gmx-users] Regarding error.

Check this page for clarification http://www.gromacs.org/Documentation/Errors#X_particles_communicated_to_PME_node_Y_are_more_than_a_cell_length_out_of_the_domain_decomposition_cell_of_their_charge_group I guess this issue was also addressed before : http://lists.gromacs.org/pipermail/gmx-user