Re: [gmx-users] I know about improper dihedrals (i.e. gi_1) , etc. Is there a way to keep phenyl rings absolutely flat.

> Hi, all, > > I need to keep a molecule absolutely flat. I know about improper > dihedrals (i.e. gi_1), but it doesn't seem to be enough to keep it > flat. It seems to get bent a little bit. I have a system with a > phenyl ring and protons and I am trying to run GROMOS 96 ff53a6 force > field.

RE: [gmx-users] velocity autocorrelation function.

On 2010-06-03 08.23, #ZHAO LINA# wrote: > Hi, > > When I looked up the manual about the autocorrelation (Chapter 8.5. > Correlation functions). There is a very general (simple) descriptions. I feel > I need a bit more deep-relevant references. > gmx_velacc.c (g_velacc) which computes the veloci

Re: [gmx-users] I know about improper dihedrals (i.e. gi_1) , etc. Is there a way to keep phenyl rings absolutely flat.

Hi, Mind not to set force constants too high, as they will introduce high frequency motions, high speeds, and decreased stability. Indeed, absolute flatness need not be required. Phenyl rings naturally come with out of plane motions. Is there reason to believe that the extent of the deformations i

RE: [gmx-users] Visualizing of a peptide in a water box - usingtrjconv

For presentations it may be the best to show first the diffusion of the protein in the box and then say that you now focus on the protein internal motions in the next slide. > -Original Message- > From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] > On Behalf Of

[gmx-users] pdb2gmx renumbers the residues in my pdb file

Hi, I'm a new gromacs user. I have encountered a problem with pdb2gmx where it automatically renumbers the residues in my pdb file. For instance, the first residue in my protein F8 has become F1 - this affects all the residues in the protein, something I find rather inconvenient. I've

Re: [gmx-users] pdb2gmx renumbers the residues in my pdb file

- Original Message - From: NG HUI WEN Date: Thursday, June 3, 2010 18:08 Subject: [gmx-users] pdb2gmx renumbers the residues in my pdb file To: gmx-users@gromacs.org --- | > Hi, > > I’m a new gromacs user. I

RE: [gmx-users] pdb2gmx renumbers the residues in my pdb file

Looks like I've got some work to do. Thanks Mark! From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham Sent: Thursday, June 03, 2010 4:27 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] pdb2gmx renumbers the residues in my pdb fi

Re: [gmx-users] pdb2gmx renumbers the residues in my pdb file

1. pdb2gmx, editconf and then solvate. 2. use trjconv and make a pdb. 3. Take 7 water molecules and put them in the top of your original pdb and start again from there. On 3 June 2010 09:34, NG HUI WEN wrote: > Looks like I’ve got some work to do. Thanks Mark! > > > > *From:* gmx-users-boun..

[gmx-users] gromacs installation and test set

Hi, all, I'm trying to install a parallel version of gromacs-4.0.7 under my own account (on our campus supercomputing center, configured with --enable-threads, --enable-float, --enable-mpi, and prefixed with specified directory), because I need to develop some new extensions for our research

[gmx-users] position restraints

Hello, I would like to restrain my molecule to a specific position in space. I would like for certain atoms to lie on the y-axis. To do this I used the following code/lines in my .top file: [ position restraints ] 2 1 1000 0 1000 ; 3 1 1000 0 1000 ; 4 1 1000 0 1000 ; 5 1 1000 0 1000 ; 6 1

Re: [gmx-users] position restraints

abdullah ahmed wrote: Hello, I would like to restrain my molecule to a specific position in space. I would like for certain atoms to lie on the y-axis. To do this I used the following code/lines in my .top file: [ position restraints ] This is an incorrect directive. It should be posit

Re: [gmx-users] gromacs installation and test set

Gu, Xiang wrote: Hi, all, I'm trying to install a parallel version of gromacs-4.0.7 under my own account (on our campus supercomputing center, configured with --enable-threads, --enable-float, --enable-mpi, and prefixed with specified directory), because I need to develop some new extension

FW: [gmx-users] position restraints

Thank you for your reply, I have been using [ position_restraints ], I do not know why it came out that way in the mail. I agree with you, the problem probably comes from the position the code lies in inside the .top file. I put it at the end of the file because I thought that was the way it

Re: [gmx-users] gromacs installation and test set

Dear Justin, (1) sorry, my ignorance; threads was enabled when installing FFTW instead of Gromacs, I should have said "configured with --enable-float and --enable-mpi" (and actually this is what I did). (2) I think I used OpenMPI. (3) Thank you. Is there anyway to fix the grompp? Xiang Jus

Re: [gmx-users] position restraints

abdullah ahmed wrote: Thank you for your reply, I have been using [ position_restraints ], I do not know why it came out that way in the mail. I agree with you, the problem probably comes from the position the code lies in inside the .top file. I put it at the end of the file because I thou

[gmx-users] extra non bonded interaction

hello I have a problem with C10O3H. The problem is that i use Trappe model and there you can add an extra repulsive interaction of molecule 10 (Oxygen) with molecule 14 (Hydrogen). The formula that TraPPE uses is 4E7/rij^12. with the transformation of 4E7in gromacs units (kJ*nm^12*mol-1) i tak

Re: [gmx-users] gromacs installation and test set

Gu, Xiang wrote: Dear Justin, (1) sorry, my ignorance; threads was enabled when installing FFTW instead of Gromacs, I should have said "configured with --enable-float and --enable-mpi" (and actually this is what I did). (2) I think I used OpenMPI. The use of "think" does not inspire con

FW: [gmx-users] position restraints

Hi! In your previous mail you mentioned: The position restraints must belong to the [moleculetype] of the species to be restrained. Once you #include a new molecule, you start a new [moleculetype] entry and the position restraints belong to it. So I rechecked my .top file and found th

Re: [gmx-users] position restraints

abdullah ahmed wrote: Hi! In your previous mail you mentioned: The position restraints must belong to the [moleculetype] of the species to be restrained. * Once you #include a new molecule, you start a new [moleculetype] entry and the position restraints belong to it. * So I rechecked my

RE: [gmx-users] position restraints

Hi, Sorry to bother you again, but I am new to gromacs and many theings don't make sense yet. I have tried reading the manual but I do not understand what you mean by "Note how the automatically-generated "posre.itp" file is #included at the end of the Protein_A moleculetype, *before* any oth

Re: [gmx-users] position restraints

Have you seen the example here? http://www.gromacs.org/Documentation/Errors#Invalid_order_for_directive_defaults What you need to do is place your [position_restraints] directive after the moleculetype to which it belongs, but before any other moleculetype has been introduced (usually by #inc

[gmx-users] 1-4 interaction not within cut-off

Hi, I set my .mdp file to minimize the system for 1000 steps, but it stopped at ~200 saying: "Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax < 10" but the molecule is now outside the box I did position restraint for 2ns using

[gmx-users] Creation of a Non-Standard Residue

I am trying to to create a non-standard residue - HCN. This cannot be done by the Dundee PRODRG server as it subsumes the polar hydrogen into the carbon. This results in a diatomic molecule that the program cannot handle. I do mind creating a new drug by hand, but a search through the email list

[gmx-users] Re: Creation of a Non-Standard Residue

I just realized a damning typo... I do NOT mind creating a new drug file by hand... is what I meant to write On Thu, Jun 3, 2010 at 11:53 AM, Mark Zottola wrote: > > I do mind creating a new drug by hand, but a search through the email list > has been less than fruitful. I have done parameter

[gmx-users] intermolecular contributions/building up a long polymer chain

Dear gmx users, Please kindly help me with the following issues: I am trying to extract interaction energies (non bonded) between hexane molecules (vdw and electrostatics). I have used rerun program to exclude intramolecular non bonded terms and here is the breakdown of energy from g_energy. Howe

Re: [gmx-users] 1-4 interaction not within cut-off

Rabab Toubar wrote: Hi, I set my .mdp file to minimize the system for 1000 steps, but it stopped at ~200 saying: "Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax < 10" but the molecule is now outside the box This is not

Re: [gmx-users] intermolecular contributions/building up a long polymer chain

Moeed wrote: Dear gmx users, Please kindly help me with the following issues: I am trying to extract interaction energies (non bonded) between hexane molecules (vdw and electrostatics). I have used rerun program to exclude intramolecular non bonded terms and here is the breakdown of energy

[gmx-users] Extracting enthalpies during or after MD

Hello, I am wondering if it is possible to output interaction energies/enthalpies during an MD simulation between specific groups of atoms. The energies are all calculated anyways before the forces are calculated, so I am wondering if there is an option to output those energies to a file? I saw

Re: [gmx-users] Extracting enthalpies during or after MD

- Original Message - From: li...@jsx.dk Date: Friday, June 4, 2010 8:47 Subject: [gmx-users] Extracting enthalpies during or after MD To: gmx-users@gromacs.org > Hello, > > I am wondering if it is possible to output interaction > energies/enthalpiesduring an MD simulation between specifi

Re: [gmx-users] Creation of a Non-Standard Residue

- Original Message - From: Mark Zottola Date: Friday, June 4, 2010 1:55 Subject: [gmx-users] Creation of a Non-Standard Residue To: Discussion list for GROMACS users > I am trying to to create a non-standard residue - HCN. This cannot be done > by the Dundee PRODRG server as it subsu

Re: [gmx-users] extra non bonded interaction

- Original Message - From: Thanasis Koukoulas Date: Thursday, June 3, 2010 23:26 Subject: [gmx-users] extra non bonded interaction To: gmx-users@gromacs.org --- | > hello > > I have a problem with C10O3H. The problem is that i use

Re: [gmx-users] Extracting enthalpies during or after MD

Hi Mark, Thanks for the quick reply. The thing with the energy groups makes sense now. But I have run into another problem with the method... The same atom cannot be in multiple energy groups during a simulation. Let say that I want the interaction energy between water and lipid head-group and

Re: [gmx-users] Creation of a Non-Standard Residue

Let me clarify. I have no problem determining the bond stretching or angle bending parameters for HCN. This was a very straightforward task. Unit conversion to get those values in a gromacs force field was also a non-issue. The problems I am having are: 1) How do I specify a POLAR hydrogen on

Re: [gmx-users] Extracting enthalpies during or after MD

- Original Message - From: li...@jsx.dk Date: Friday, June 4, 2010 10:35 Subject: Re: [gmx-users] Extracting enthalpies during or after MD To: Discussion list for GROMACS users > Hi Mark, > > Thanks for the quick reply. > > The thing with the energy groups makes sense now. But I have

Re: [gmx-users] Creation of a Non-Standard Residue

- Original Message - From: Mark Zottola Date: Friday, June 4, 2010 10:40 Subject: Re: [gmx-users] Creation of a Non-Standard Residue To: Discussion list for GROMACS users > Let me clarify. > > I have no problem determining the bond stretching or > angle bending parameters for HCN.

Re: [gmx-users] Creation of a Non-Standard Residue

Mark Zottola wrote: Let me clarify. I have no problem determining the bond stretching or angle bending parameters for HCN. This was a very straightforward task. Unit conversion to get those values in a gromacs force field was also a non-issue. The problems I am having are: 1) How do

Re: [gmx-users] Creation of a Non-Standard Residue

- Original Message - From: Mark Abraham Date: Friday, June 4, 2010 11:51 Subject: Re: [gmx-users] Creation of a Non-Standard Residue To: Discussion list for GROMACS users > > > - Original Message - > From: Mark Zottola > Date: Friday, June 4, 2010 10:40 > Subject: Re: [gmx-u

[gmx-users] Is there a way to energy minimize only part of macromolecular structure?

Hi, all, Is there a way to energy minimize only part of the structure? I have made the ndx file, but I am not sure what parameters to use with mdrun. Your help is much appreciated. Art Dr. Arthur Roberts, Ph.D. University of California, San Diego Skaggs School of Pharmacy and Pharmaceuti

[gmx-users] After simulated annealing and then energy minimizing, a docked molecule seems to still be distorted?

Hi, All, I am doing simulated annealing of a docked molecule. Because of vibrational modes, the aromatic rings are somewhat distorted. I tried energy minimization afterwords, but I can't seem to get the distortions out of the rings. Is there a way to energy minimize, so that the geomet

Re: [gmx-users] Is there a way to energy minimize only part of macromolecular structure?

- Original Message - From: Arthur Roberts Date: Friday, June 4, 2010 13:57 Subject: [gmx-users] Is there a way to energy minimize only part of macromolecular structure? To: gmx users > Hi, all, > > Is there a way to energy minimize only part of the > structure? I have made the ndx

[gmx-users] Regarding genconf

Hello, I build a system solvated in water . Then replicated the system using genconf. Now when I am running grompp i am getting following warning Warning: atom name 404 in PH7.top and replicate_systemB.gro does not match (N - C1) Warning: atom name 405 in PH7.top and replicate_systemB.gro does not

[gmx-users] RE:Blowing up follow-up

Dear All, I had posted a couple days ago reguarding my system blowing up, after energy minimizing the structure, adding waters, then adding ions. I had repeated this from scratch several times as per the instructions, and played with everything possible in the .mdp files. I noticed in visual