Re: [gmx-users] Regarding conversion of C6/C12 parameters to sigma/epsilon

naga raju wrote: Dear gmx users, I have one doubt regarding conversion of C6/C12 parameters to sigma /epsilon. I added atomtypes, pairtypes and dihedraltypes from lipid.itp to ffoplsaanb.itp---after changing C6/C12 paramters to sigma/epsilon as given in mailing list (http://www.gr

Re: [gmx-users] Fatal error:Atom S in residue TYR 2 not found in rtp entry with 18 atoms

Hi Winter, I'm a beginner to GMX, when I use the following command: "pdb2gmx -f 1G1S.pdb -p gr.top -o gr.gro -missing" Don't use '-missing'. Since you're a beginner you're not allowed to (unless you get a permit for it from one of the developers). "WARNING: atom CD not found in residue 72 wh

Re: [gmx-users] Very large fluctuations in dg/dl

Hi Berk, Just a question relating to your reply (should be a new thread maybe...). The Gromos force fields were parameterized (for use) with cutoff/RF. PME is of course better for energy conservation, but the inclusion of the interactions beyond the cut-off may give rise to deviant behaviour from

[gmx-users] Regarding conversion of C6/C12 parameters to sigma/epsilon

Dear gmx users, I have one doubt regarding conversion of C6/C12 parameters to sigma /epsilon. I added atomtypes, pairtypes and dihedraltypes from lipid.itp to ffoplsaanb.itp---after changing C6/C12 paramters to sigma/epsilon as given in mailing list (http://www.gromacs.org/pipermail/

RE: [gmx-users] Visualization Problem

Probably means that atoms are moving across the pbc boundary from one side of the box to another. The visualiser you are using is trying to maintain the bond between the atoms after the move, so draws it all the way across the box itself. Two ways to fix, don't visualise the bonds, using either p

Re: [gmx-users] Visualization Problem

Thanks Itamar for your reply, but the tube actually does not jump, but the lines showing the bonds start to show bonding between non-neighbouring atoms, i.e., the hexagonal shape characteristic of nanotubes is destroyed, and it starts from the third frame regardless of the start time. I tried t

Re: [gmx-users] Visualization Problem

Shalom George Maybe your nanotube 'jump' over the PBC? Try 'trjconv -pbc whole ...' Best, Itamar George Abadir wrote: Hi, I finished a simulation of a carbon nanotube in water. I made a movie of the simulation using 'trjconv' to view with Pymol. The problem is that starting from the thi

[gmx-users] Fatal error:Atom S in residue TYR 2 not found in rtp entry with 18 atoms

Hi all, I'm a beginner to GMX, when I use the following command: "pdb2gmx -f 1G1S.pdb -p gr.top -o gr.gro -missing" "WARNING: atom CD not found in residue 72 while adding improper Fatal error: Atom S in residue TYR 2 not found in rtp entry with 18 atoms while sorting atoms" How

[gmx-users] Visualization Problem

Hi, I finished a simulation of a carbon nanotube in water. I made a movie of the simulation using 'trjconv' to view with Pymol. The problem is that starting from the third frame it messes the carbon nanotube bonds. I changed the start time and again in the third frames it messed things up.

Re: [gmx-users] Problems using grompp and amber force field

Hi, With regards to the versions you are correct, ffamber_v3.3.1 is for use with Gromacs 3.3.1. As for the error i would suggest you do what Mark says and make sure all your inclusions are correct. If you still can't find the problem then you need to post some of your .top file so we can have

Re: [gmx-users] Cys-Cys Bond

fulya caglar wrote: Hi everone. I'm studying on a protein including two chains with *four* disulfide bonds.when I watched the simulation I saw that A and B chains were splitting from eachother. Check your topology. This will mean that you didn't define the disulfides in the first place. You

Re: [gmx-users] (no subject)

vijaya subramanian wrote: Hi I ran an md simulation on speptide, the tutorial example. The reference temperature in the mdp file is 300 K but I find the system equilibrates to 305 K. Why is this? Is this an average or the final temperature? Mark

Re: [gmx-users] Problems using grompp and amber force field

root wrote: Dear GROMACS user: Erik and Tom thanks by the comments, too. Sorry, I read the FAQ pages of http://folding.stanford.edu and now I understand your comments. We tried with cpp = /lib/cpp -traditional in the mdp file. The warning desapears, but the error messages is similar. (Fatal e

Re: [gmx-users] Problems using grompp and amber force field

Dear GROMACS user: Erik and Tom thanks by the comments, too. Sorry, I read the FAQ pages of http://folding.stanford.edu and now I understand your comments. We tried with cpp = /lib/cpp -traditional in the mdp file. The warning desapears, but the error messages is similar. (Fatal error: > >> Atom

[gmx-users] (no subject)

Hi I ran an md simulation on speptide, the tutorial example. The reference temperature in the mdp file is 300 K but I find the system equilibrates to 305 K. Why is this? VS _ Watch free concerts with Pink, Rod Stewart, Oasis and

Re: [gmx-users] Problems using grompp and amber force field

As someone already mentioned, the following can be found among the AMBERport FAQ: >> Why do I get a grompp warning "missing white space after `#define proper_*'?" Set "cpp = /lib/cpp -traditional" in your .mdp file to remove these warnings, which result from the use of the N* atom type of t

Re: [gmx-users] Problems using grompp and amber force field

David and GROMACS users: Sorry we changed the error message in ... /usr/local/gromacs/share/top/ffamber03bon.itp:541:22: warning: spaces are absent in target after the name of macro because of the original message was in spanish. We checked these files above. We run GROMACS in fedora 6.

[gmx-users] Very large fluctuations in dg/dl

Hi Patrick, I find a reasonable DeltaGsol value of 8.6 kJ/mol for methane (compared to 8.7 in Geerke & van Gunsteren, ChemPhysChem 2006, 7, 671 – 678) but I get really huge fluctuations in the values of dg/dl: lambda=0.00: 5.0 +/- 10.8 (mean +/- standard deviation) lambda=0.05: 4.3 +/- 11.2

Re: [gmx-users] Problems using grompp and amber force field

Hi, I think if you set "cpp = /lib/cpp -traditional" in your .mdp file then it should get rid of the warnings about "spaces are absent in target after the name of macro". For more info see Tom --On 07 May 2007 20:42 +0200 David van der Spoel <[

[gmx-users] Cys-Cys Bond

Hi everone. I'm studying on a protein including two chains with four disulfide bonds.when I watched the simulation I saw that A and B chains were splitting from eachother.Then I gave that command. pdb2gmx-f 1ppbfree.pdb -p 1ppbfree.top -o 1ppbfree.gro -merge -ss -inter -ignh. But

Re: [gmx-users] Problems using grompp and amber force field

root wrote: Dear GROMACS user: David and Mark, thanks by our comments, suggestions and questions. If our response is confused, please require us copies of output files (or fragment). The procedure to simulate the DNA dodecamer was: 1) We generate the DNA topology and coordinates in gromacs fo

[gmx-users] Problems using grompp and amber force field

Dear GROMACS user: David and Mark, thanks by our comments, suggestions and questions. If our response is confused, please require us copies of output files (or fragment). The procedure to simulate the DNA dodecamer was: 1) We generate the DNA topology and coordinates in gromacs format (with the

RE: [gmx-users] Very large fluctuations in dg/dl

From: Patrick Fuchs <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: gmx-users@gromacs.org Subject: [gmx-users] Very large fluctuations in dg/dl Date: Mon, 07 May 2007 16:41:26 +0200 Hi Gromacs users, I have a few questions related to solvation free energy calculation via

[gmx-users] Very large fluctuations in dg/dl

Hi Gromacs users, I have a few questions related to solvation free energy calculation via thermodynamic integration. I'm trying to reproduce some literature data (on e.g. methane, methanol...) using the GROMOS G53a6 force field. I followed the tutorial of David Mobley (thanks to him BTW), but I us

Re: [gmx-users] Targeted Molecular dynamics

I have implemented one approach to targeted MD for version 3.2.1 that uses soft restraints to achieve the transformation. We imagined we would make the code available (contribute it to Gromacs) after we submit the manuscript. Jay -- R. Jay Mashl University of Illinois [EMAIL PROTECTED] (Te

[gmx-users] Regarding DOPC lipid parameters

Dear gmx users, I have one doubt regarding conversion of C6/C12 parameters to sigma /epsilon. As Mr Chris neale said (http://www.gromacs.org/pipermail/gmx-users/2006-May/021416.html ), I added atomtypes, pairtypes and dihedraltypes from lipid.itp to ffoplsaanb

[gmx-users] Regarding conversion of C6/C12 parameters in .itp file

Dear gmx users, I have one doubt regarding conversion of C6/C12 parameters to sigma /epsilon. As Mr Chris neale said (http://www.gromacs.org/pipermail/gmx-users/2006-May/021416.html ), I added atomtypes, pairtypes and dihedraltypes from lipid.itp to ffoplsaanb

RE: [gmx-users] Re: Energy conservation of crystal surface(specification)

From: Janne Hirvi <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: gmx-users@gromacs.org Subject: [gmx-users] Re: Energy conservation of crystal surface(specification) Date: Mon, 7 May 2007 14:44:34 +0300 >>Hello again! >> >>In earlier message I said that double precisi

[gmx-users] Re: Energy conservation of crystal surface (specification)

>>Hello again! >> >>In earlier message I said that double precision (actually same with single >>precision) simulation with 4 processors terminates pretty soon and distinct >>momentary increases in energy at intervals of 0.05ps can be observed until >>that point. >> >>Now I have made more tests an

Re: [gmx-users] Targeted Molecular dynamics

From: Mark Abraham <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: Discussion list for GROMACS users Subject: Re: [gmx-users] Targeted Molecular dynamics Date: Mon, 07 May 2007 21:20:23 +1000 Olivier Perin wrote: Dear gmx users, OBJECT: I just contact you to confirm on

Re: [gmx-users] Targeted Molecular dynamics

Olivier Perin wrote: Dear gmx users, OBJECT: I just contact you to confirm one thing about the ability to run a targeted molecular dynamic simulation with gromacs with the help of positional restraints. SITUATION: If struct1 and struct2 are two near conformations of one same protein could I

[gmx-users] Targeted Molecular dynamics

Dear gmx users, OBJECT: I just contact you to confirm one thing about the ability to run a targeted molecular dynamic simulation with gromacs with the help of positional restraints. SITUATION: If struct1 and struct2 are two near conformations of one same protein could I use these two gromacs

RE: [gmx-users] Energy conservation of crystal surface (specification)

From: Janne Hirvi <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: gmx-users@gromacs.org Subject: [gmx-users] Energy conservation of crystal surface (specification) Date: Mon, 7 May 2007 12:25:17 +0300 Hello again! In earlier message I said that double precision (actuall

[gmx-users] Energy conservation of crystal surface (specification)

Hello again! In earlier message I said that double precision (actually same with single precision) simulation with 4 processors terminates pretty soon and distinct momentary increases in energy at intervals of 0.05ps can be observed until that point. Now I have made more tests and noticed that a

Re: [gmx-users] Positive and negative ions move in the same direction under a constant electric field?

林揚善 wrote: > tc_grps =SOL NA+CL- > > tau_t =0.1 0.1 0.1 > > ref_t =300 300 300 I don't know if it's germane to your problem, but this is about the tenth time this month that someone has reported an .mdp file with groups

[gmx-users] Positive and negative ions move in the same direction under a constant electric field?

Dear all： In order to make sure that my procedure for applying electric field using Gromacs is correct, I applied electric fields to sodium chloride solvent (SPC216.pdb with NA+ and CL-) in the x direction. After 2 ns running, the trajectories of ions and water molecules showed that both