Re: [gmx-users] Charge grps and cut-off

Sai Pooja wrote: Hi, I am trying to reproduce results from a paper which uses this cutoff. The work is on loop-folding and they use implicit solvent. I am using explicit solvent with charmm 27. Below is my mdp file. I am not sure if there is any advantage in using a large cut-off. Larg

Re: [gmx-users] Charge grps and cut-off

Hi, I am trying to reproduce results from a paper which uses this cutoff. The work is on loop-folding and they use implicit solvent. I am using explicit solvent with charmm 27. Below is my mdp file. I am not sure if there is any advantage in using a large cut-off. ; VARIOUS PREPROCESSING OPTIONS

Re: [gmx-users] Charge grps and cut-off

Sai Pooja wrote: Hi, I am getting these notes when I run grompp: NOTE 3 [file Init/ffsb_init.top]: The largest charge group contains 12 atoms. Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large char

Re: [gmx-users] frezzing a bond

Nilesh Dhumal wrote: Hello, I am trying to freeze a bond (3.5 A) in my system. I used the index file to define group and I added this two lines in my .mdp file. freezegrps = PA NE freezedim = Y Y Y Y Y Y I used g_dist to verify the distance between the freezing atoms and it turned

Re: [gmx-users] Need For a Script

Samrat Pal wrote: Dear All, I am a new GROMACS user. I have been able to solvate a protein in a water box and also to simulate it and unfold it by heating it. But I have facing problem with the script of AFM pulling. I want to unfold a protein by pulling the two ends of the protein. Can

[gmx-users] Charge grps and cut-off

Hi, I am getting these notes when I run grompp: NOTE 3 [file Init/ffsb_init.top]: The largest charge group contains 12 atoms. Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large charge groups can lead

[gmx-users] frezzing a bond

Hello, I am trying to freeze a bond (3.5 A) in my system. I used the index file to define group and I added this two lines in my .mdp file. freezegrps = PA NE freezedim = Y Y Y Y Y Y I used g_dist to verify the distance between the freezing atoms and it turned out 3.9 A. I checked my

[gmx-users] Need For a Script

Dear All, I am a new GROMACS user. I have been able to solvate a protein in a water box and also to simulate it and unfold it by heating it. But I have facing problem with the script of AFM pulling. I want to unfold a protein by pulling the two ends of the protein. Can anyone give me a full

Re: [gmx-users] Avoid generation of angles, pairs and dihedrals from pdb2gmx

You can just delete them in the generated top file. dawei On Fri, Jul 16, 2010 at 10:45 AM, C. Batistakis wrote: > Dear all > > According to the manual, pdb2gmx generates all the angles, pairs and > dihedrals automatically in a polymer chain. Because I need nothing of them > do you know any fas

[gmx-users] Avoid generation of angles, pairs and dihedrals from pdb2gmx

Dear all According to the manual, pdb2gmx generates all the angles, pairs and dihedrals automatically in a polymer chain. Because I need nothing of them do you know any fast way to avoid this generation? The only think I found in the manual is to add [ exclusions ] in the .rtp file for whateve

[gmx-users] Re: Selecting a force field for dioxane

Dear banskt: I would take the LJ(12,6) parameters from AMBER and calculate the electrostatic charges using RESP - http://q4md-forcefieldtools.org/RED/ . Just what I would start with personally. Dr. Vitaly Chaban > I would like to know if anybody has reproduced the physical properties of > dioxa

[gmx-users] g_lie query

Hi ALL, I have run a protein + ligand (dopamine) simulation. Now I want to calculate the free energy of binding using g_lie. But g_lie asks for two values: Elj and Eqq. How or from where can I get these values for my ligand? Also, do I need to run a simulation with only the ligand? And, is there a

Re: [gmx-users] Selecting a force field for dioxane

Saikat Banerjee wrote: Hi, I would like to know if anybody has reproduced the physical properties of dioxane (like dielectric constant, dipole moment, etc) in GROMACS. If so, what force field was found to be optimum? If not, then anybody has any idea about which force field to start with?

Re: [gmx-users] to visualise protein conformation after every 1ns

sonali dhindwal wrote: ok, 4 files, my mistake, I checked all the files and they have RMSD among themselves of 2-3 Angstrom, can you please explain it why it is so ? Why wouldn't they? Are you expecting them to be the same? You won't get much in the way of an explanation for most questions

[gmx-users] Selecting a force field for dioxane

Hi, I would like to know if anybody has reproduced the physical properties of dioxane (like dielectric constant, dipole moment, etc) in GROMACS. If so, what force field was found to be optimum? If not, then anybody has any idea about which force field to start with? Thanking you, banskt -- ---

Re: [gmx-users] to visualise protein conformation after every 1ns

ok, 4 files, my mistake, I checked all the files and they have RMSD among themselves of 2-3 Angstrom, can you please explain it why it is so ? Thanks -- Sonali Dhindwal --- On Fri, 16/7/10, Oliver Grant wrote: From: Oliver Grant Subject: Re: [gmx-users] to visualise protein conformation after

RE: [gmx-users] scripting question

Thanks alot Rui for the hint From: gmx-users-boun...@gromacs.org on behalf of J. Rui Rodrigues Sent: Fri 7/16/2010 3:26 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] scripting question google: for loop bash On Fri, 16 Jul 2010 02:57:12 -070

Re: [gmx-users] inversion of lipid bilayer with water in the centre

ram bio wrote: Dear Gromacs Users, I have a lipid bilayer with me and I would like to simulate a system by keeping the water molecules with proteins in it and lipid surrounding the water on both sides, can any body suggest me please... If you place the bilayer at the "bottom" of the unit c

Re: [gmx-users] how to write a frames.ndx for -fr option of trjconv

Hassan Shallal wrote: Dear Gromacs users, I need trjconv to write me pdb files at a list of frames that are randomly chosen throughout the whole production trajectory (they belong to the least energetic 100 frames). I can use trjconv to write a pdb at each frame but this is gonna be time c

Re: [gmx-users] scripting question

google: for loop bash On Fri, 16 Jul 2010 02:57:12 -0700, Hassan Shallal wrote > Dear Gromacs users, > > This question is much more of a unix/linux scripting issue. Let's say I have > 10 pdb files named mt_1.pdb, mt_2.pdb, .mt_10.pdb. If I need to energy > minimize the 10 pdb files using th

Re: [gmx-users] to visualise protein conformation after every 1ns

0ns, 1ns, 2ns and 3ns gives four files. On 16 July 2010 10:47, sonali dhindwal wrote: > Thanks Tsjerk, > I was confused, that why 3 files are generated as output. I will check it. > I appreciate what you said, I will read more. > Regards > > -- > Sonali Dhindwal > > > --- On *Fri, 16/7/10, Tsjer

[gmx-users] scripting question

Dear Gromacs users, This question is much more of a unix/linux scripting issue. Let's say I have 10 pdb files named mt_1.pdb, mt_2.pdb, .mt_10.pdb. If I need to energy minimize the 10 pdb files using the same em.mdp and the same mt.top file, how can I create a script for minimizing the 10 f

Re: [gmx-users] to visualise protein conformation after every 1ns

Thanks Tsjerk, I was confused, that why 3 files are generated as output. I will check it. I appreciate what you said, I will read more. Regards -- Sonali Dhindwal --- On Fri, 16/7/10, Tsjerk Wassenaar wrote: From: Tsjerk Wassenaar Subject: Re: [gmx-users] to visualise protein conformation afte

[gmx-users] inversion of lipid bilayer with water in the centre

Dear Gromacs Users, I have a lipid bilayer with me and I would like to simulate a system by keeping the water molecules with proteins in it and lipid surrounding the water on both sides, can any body suggest me please... Thanks Ram -- gmx-users mailing listgmx-users@gromacs.org http://list

[gmx-users] g_lie query

Hi ALL, I have run a protein + ligand (dopamine) simulation. Now I want to calculate the free energy of binding using g_lie. But g_lie asks for two values: Elj and Eqq. How or from where can I get these values for my ligand? Also, do I need to run a simulation with only the ligand? And, is there a

[gmx-users] how to write a frames.ndx for -fr option of trjconv

Dear Gromacs users, I need trjconv to write me pdb files at a list of frames that are randomly chosen throughout the whole production trajectory (they belong to the least energetic 100 frames). I can use trjconv to write a pdb at each frame but this is gonna be time consuming, so I looked in

Re: [gmx-users] to visualise protein conformation after every 1ns

Sonali, Why wouldn't it be correct if you did just what David told you to do? And how would you be able to check yourself whether you were correct? We can't hold your hand here for every step you make. Have you already gone through the tutorial material linked on the Gromacs website? If not, pleas

Re: [gmx-users] to visualise protein conformation after every 1ns

Hello Sir, Thanks for the reply, I tried to run this commad on a simuation which I started to ran for 10 ns,and has already completed around 3 ns I gave trjconv -o 1ns.pdb -dt 1000 -s topol.tpr -f traj.xtc -sep after this it asked for selecting which one I want among, System, protein,bacakbone,c

Subject: [gmx-users] to visualise protein conformation after every 1ns

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Re: [gmx-users] to visualise protein conformation after every 1ns

On 7/16/10 9:02 AM, sonali dhindwal wrote: Hello All, Sorry for a dumb question,,but I have a query that I want to run a 5 ns simulation on one of the protein and I want to see protein's conformation after every 1 ns,i.e to have a pdb file, so how should I proceed or changes should I make in mdp

[gmx-users] to visualise protein conformation after every 1ns

Hello All, Sorry for a dumb question,,but I have a query that I want to run a 5 ns simulation on one of the protein and I want to see protein's conformation after every 1 ns,i.e to have a pdb file, so how should I proceed or changes should I make in mdp file. Thanks -- Sonali Dhindwal -- gmx-