[gmx-users] Re:gmx-users Digest, Vol 67, Issue 150 memory allocation

hai justin,ya i am working on actual KALP tutorial onlyhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmxtutorials/membraneprotein/index.htmland i am using the pdb file which is given in the website. This is the first time i am doing MD simulation for transmembrane proteins before usi

[gmx-users] Re:gmx-users Digest, Vol 67, Issue 150

hai justin,ya i am working on actual KALP tutorial onlyhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmxtutorials/membraneprotein/index.htmland i am using the pdb file which is given in the website. This is the first time i am doing MD simulation for transmembrane proteins before usi

Re: [gmx-users] trjconv -pbc cluster with rhombic dodecahedron box

Hi, > trjconv -f a.xtc -o a_cluster.gro -e 0.001 -pbc cluster You might want to use -dump to extract a specific frame, rather than using -e: trjconv -f a.xtc -o a_cluster.gro -pbc cluster -dump 0 Also, do mind that for a subsequent call to trjconv, using -pbc nojump and the extracted frame as r

[gmx-users] topolbuild

Hi List, I have downloaded topolbuild1.2.1 but cannot extract files. Can anyone help and check the link? Many thanks -- Regards, Neha Gandhi Gajaria, School of Biomedical Sciences, Curtin University of Technology, GPO Box U1987 Perth, Western Australia 6845 -- gmx-users mailing listgmx-use

[gmx-users] g_mindist , trajectory only CA atoms, to small values?

Dear Gromacs users, my system consist of two parts, which are not connected. My system has around 10 atoms. To make the trajectory handling and the analysis more feasible I store only the CA atoms in the xtc trajectory. I want to use the "g_mindist" command to calculate the minimal distance

[gmx-users] trjconv -pbc cluster with rhombic dodecahedron box

Hi Daniel, I think you still need to read and attempt what has already been suggested. To be more explicit: trjconv -f a.xtc -o a_cluster.gro -e 0.001 -pbc cluster grompp -f a.mdp -c a_cluster.gro -o a_cluster.tpr trjconv -f a.xtc -o a_cluster.xtc -s a_cluster.tpr -pbc nojump from: http://li

Re: [gmx-users] gromp error for gmxtest-4.0.4 and 3.3.3 on new gromacs-4.0.5 install

mrshi...@gmail.com wrote: What other input might you need for a test set? As a minor developer and a stickler for accuracy, I would be very much interested in the sorts of inputs your looking for, and have some ideas as well. There's a number of issues listed in the posts in the URLs below, ch

[gmx-users] Tensor of inertia moments at each time step

Hi, Is it possible in GROMACS to extract from trajectory file 9 components of tensor of inertia moments at each time step? I know that it is possible to extract 3 vectors, but not whole tensor. Any suggestions? Thank you Egis --- On Tue, 12/1/09, gmx-users-requ...@gromacs.org wrote: > From

Re: [gmx-users] Fwd: Last step before CG em.mdp

Justin A. Lemkul wrote: Then that's certainly the first problem to fix. This is why I generally use editconf for defining the box (and why I keep recommending it). For a simple protein in water, using a command like: editconf -c -d 1.0 will define a suitably-sized box so that you don't h

Re: [gmx-users] Fwd: Last step before CG em.mdp

Francesco Pietra wrote: On Mon, Nov 30, 2009 at 8:18 PM, Justin A. Lemkul wrote: Francesco Pietra wrote: Failed to specify that both the DPPC bilayer and the box of water are from equilibrated systems in MARTIN web, while the protein was Amber minimized (and MD) before generating the CG. I

Re: [gmx-users] Problem with output structures generated by energy minimization with GROMACS 4

Tsjerk, Thanks for your reply. I am doing a simple test case with 500 SPC/E water molecules. First I did minimization with steepest decent, using a command like mdrun -pd -s water.gro.tpr -c final.gro The generated md.log looks like the following: Step

Re: [gmx-users] Fwd: Last step before CG em.mdp

On Mon, Nov 30, 2009 at 8:18 PM, Justin A. Lemkul wrote: > > > Francesco Pietra wrote: >> >> Failed to specify that both the DPPC bilayer and the box of water are >> from equilibrated systems in MARTIN web, while the protein was Amber >> minimized (and MD) before generating the CG. >> >> I have tr

Re: [gmx-users] Tabulated potentials make newbies crazy

ms wrote: Mark Abraham ha scritto: > Sorry, I was a bit incomplete last night. Charge groups are the fundamental unit for neighbour-searching (3.4.2) to construct lists of charge groups for nonbonded interactions, which determine lists of atom-atom interactions. However, the nonbonded interacti

Re: [gmx-users] amber force field in Gromacs

servaas wrote: Hello, I tried using the amber force field in GROMACS. I proceeded as follows: Determined my parameters with RED/ANTECHAMBER/tleap converted them with amb2gmx.pl (or with acpypi, problem is the same) to gromacs coordinate and topology files. It concerns a modified nucleotide. I m

Re: [gmx-users] Fwd: Last step before CG em.mdp

Francesco Pietra wrote: Failed to specify that both the DPPC bilayer and the box of water are from equilibrated systems in MARTIN web, while the protein was Amber minimized (and MD) before generating the CG. I have tried the cg protein alone genbox -cp my.pdb -box 15 -o my.gro Again I ask

[gmx-users] Fwd: Last step before CG em.mdp

Failed to specify that both the DPPC bilayer and the box of water are from equilibrated systems in MARTIN web, while the protein was Amber minimized (and MD) before generating the CG. I have tried the cg protein alone genbox -cp my.pdb -box 15 -o my.gro grompp -f em.mdp -c my.gro -p my.top -o to

Re: [gmx-users] gromacs error

pawan raghav wrote: I am using Gromacs on windows hen executing pdb2gmx command, I got an error i.e. Fatal error: Atom HD1 in residue HISB 3 not found in rtp entry with 14 atoms while sorting atoms. May be different protonation state. Remove this hydrogen or choose a different protonation s

Re: [gmx-users] trjconv -pbc cluster with rhombic dodecahedron box

Hi Daniel, If the structure is correct in the coordinate file you used as input to generate the .tpr, you can use that structure as reference to trjconv, using -pbc nojump. Cheers, Tsjerk On Mon, Nov 30, 2009 at 6:17 PM, Daniel Parton wrote: > Hi, > > Thanks for the suggestion to use trjconv -

Re: [gmx-users] Problem with output structures generated by energy minimization with GROMACS 4

Ni Hao, You don't give too much information here. What exactly are you doing? What are the commands? What's the difference between the first and the second pass of EM? One thing to check is whether the output/input file has a correct box definition. Cheers, Tsjerk 2009/11/30 HAO JIANG : > Hi, >

[gmx-users] trjconv -pbc cluster with rhombic dodecahedron box

Hi, Thanks for the suggestion to use trjconv -pbc nojump. Unfortunately, it has not worked, as the vesicle is still not whole in the trajectory. I have tried subsequently centering the trajectory, and representing the system with -ur compact, but still it does not work. I am wondering if the

[gmx-users] Problem with output structures generated by energy minimization with GROMACS 4

Hi, I got a problem with the output structure files (gro/trr/xtc) generated by the energy minimization with GROMACS 4. That is, when I used the generated structure as the input for further minimizations or MD simulations, I got very large potential energy and forces at step 0, as if the structu

[gmx-users] gromacs error

I am using Gromacs on windows hen executing pdb2gmx command, I got an error i.e. Fatal error: Atom HD1 in residue HISB 3 not found in rtp entry with 14 atoms while sorting atoms. May be different protonation state. Remove this hydrogen or choose a different protonation state. I want to know what

Re: [gmx-users] Last step before CG em.mdp

Francesco Pietra wrote: Hi: This is to ask how to proceed to minimize a CG ensemble made of a transmembrane multimer with pore region immersed in a hydrated DPPC bilayer and extracellular region immersed in water. Total height 18 nm, width 10 nm in the extracellular region and 6 nm in the pore

[gmx-users] Last step before CG em.mdp

Hi: This is to ask how to proceed to minimize a CG ensemble made of a transmembrane multimer with pore region immersed in a hydrated DPPC bilayer and extracellular region immersed in water. Total height 18 nm, width 10 nm in the extracellular region and 6 nm in the pore region. No clashes/contacts

Re: [gmx-users] free energy calculations using MBAR and gromacs

This looks like more of a pymbar question! >  I am trying to calculate free energy of a system that involves > disappearance of LJ particle at lambda=1 in explicit solvent. I ran the > simulation at 20 different lambda points ranging from 0 to 1, using soft > core potential. In order to use MBAR m

[gmx-users] Survey: 3 minutes of your time

Hello, My name is Pieter van 't Hof. As part of my Master thesis in computer science I am currently extending Gromacs and VMD to visualize short range Lennard Jones potentials and Coulomb forces during interactive molecular dynamics simulations. In order to choose a representation method which is

[gmx-users] Survey: 3 minutes of your time

Hello, My name is Pieter van 't Hof. As part of my Master thesis in computer science I am currently extending Gromacs and VMD to visualize short range Lennard Jones potentials and Coulomb forces during interactive molecular dynamics simulations. In order to choose a representation method which is

[gmx-users] amber force field in Gromacs

Hello, I tried using the amber force field in GROMACS. I proceeded as follows: Determined my parameters with RED/ANTECHAMBER/tleap converted them with amb2gmx.pl (or with acpypi, problem is the same) to gromacs coordinate and topology files. It concerns a modified nucleotide. I minimized with s

Re: [gmx-users] gmx-users Digest, memory allocation error

hema dhevi wrote: hi justin, thanks for your reply Totally I have 6126 atoms (residues + DPPC ) I am using the same pdb file and lipid pdb (DPPC-128) which is given in the KAPL tutorial. OK, just to clarify - are you working on the actual KALP tutorial when this error comes up, or are yo

[gmx-users] trjconv -pbc cluster with rhombic dodecahedron box

Hi Daniel, what Tsjerk has suggested is really the only way to go here. If your cluster is not whole in the first frame, you can do it this way: 1. use trjconv -pbc cluster to make your cluster whole in a frame near the start of your trajectory. If the first frame enters the infinite loop

Re: [gmx-users] Re: How to make carbon nanotube infinite?

Cun Zhang wrote: hi, Justin. Thank you for your meticulous and patient explanation ! Before I see this post, I misunderstood the meaning of sharing bonds. I thought note only the bonds,but also the angles and the dihedrals should be added to top file. I see now that I should have been more

Re: [gmx-users] trjconv -pbc cluster with rhombic dodecahedron box

Hi Daniel, This doesn't exactly answer your question, but if your vesicle is whole at the start, can't you better keep it that way using -pbc nojump? If necessary, you can also recenter afterwards. Hope it helps, Tsjerk On Mon, Nov 30, 2009 at 12:24 PM, Daniel Parton wrote: > Hi, > > I am runn

Re: [gmx-users] Tabulated potentials make newbies crazy

Mark Abraham ha scritto: > Sorry, I was a bit incomplete last night. Charge groups are the > fundamental unit for neighbour-searching (3.4.2) to construct lists of > charge groups for nonbonded interactions, which determine lists of > atom-atom interactions. However, the nonbonded interactions are

Re: [gmx-users] Gromacs with QMMM Support

Thanks. I see MOPAC7 is in the public domain. That way I can use it on my project! 1 The original copyright notice of MOPAC7: 2 3 C 4 C Notice of Public Domain nature of MOPAC 5 C 6 C 'This computer program is a work of the United States 7 C Governmen

[gmx-users] trjconv -pbc cluster with rhombic dodecahedron box

Hi, I am running a coarse-grained simulation of a lipid vesicle (~70,000 particles), using a rhombic dodecahedron box to limit the amount of solvent I require. The vesicle (unsurprisingly) moves over the periodic boundaries during the simulation. Various analyses I am conducting require the

[gmx-users] Re: How to make carbon nanotube infinite?

hi, Justin. Thank you for your meticulous and patient explanation ! Before I see this post, I misunderstood the meaning of sharing bonds. I thought note only the bonds,but also the angles and the dihedrals should be added to top file. It was so complicated to deal manually that I wrote that scri

[gmx-users] NPT REMD

Hello everyone, I'm trying to perform REMD simulation at NPT emsemble. Here I have some question. 1) Using parrinello-rahman pressure coupling, REMD simulation is unstable at high temperature. (highest temperature ~400K). 2) Using berendsen T-coupling and P-coupling scheme..(tau_t = 0.1ps