[gmx-users] Re: efficient use of pme with gromacs

Hi Léo, please keep Gromacs-related issues on the Gromacs-users mailing list. This will give others with similar problems the possibility to profit from already answered questions by searching this list. Also, please choose a descriptive subject (I have done that for you). Thank you! The messag

[gmx-users] Energy minimisation problems - coordinate file and topology file not matching.

Hi everyone, I was hoping you could clear up a problem I'm having when performing energy minimisation. I'm following the instructions from one of the tutorials (Justin's Umbrella Sampling) with my own protein, however, this time when I try to perform the energy minimisation it throws out this

Re: [gmx-users] Energy minimisation problems - coordinate file and topology file not matching.

Hi, Natalie, Obviously, number of coordinates still doesn't match the topology file even you updated the topol.top *carefully*. Check the topol.top thoroughly or paste several line of your coordinate and topology files may be good ideas. Note that the topology file is lacking information for *28*

Re: [gmx-users] Energy minimisation problems - coordinate file and topology file not matching.

Natalie Stephenson wrote: Hi everyone, I was hoping you could clear up a problem I'm having when performing energy minimisation. I'm following the instructions from one of the tutorials (Justin's Umbrella Sampling) with my own protein, however, this time when I try to perform the energy mi

RE: [gmx-users] Energy minimisation problems - coordinate file and topology file not matching.

Thanks for your help Justin & Terry I've been letting genion etc update it ... so there must be somewhere where i've missed it or something. I'll check through the files and see if I can see what's missing... xxx From: gmx-users-boun...@gromacs.org [gmx-users-

RE: [gmx-users] Energy minimisation problems - coordinate file and topology file not matching.

Ok ... think I've worked out what's happened ... There were two 'SOL' groups. So when replacing solvent with ions it has added double the amount of ions to the topol.top file. Think I'll go back a couple of steps and try to sort out why there are two 'SOL' groups. Thanks for the help! xxx ___

Re: [gmx-users] Energy minimisation problems - coordinate file and topology file not matching.

Natalie Stephenson wrote: Ok ... think I've worked out what's happened ... There were two 'SOL' groups. So when replacing solvent with ions it has added double the amount of ions to the topol.top file. Think I'll go back a couple of steps and try to sort out why there are two 'SOL' groups.

RE: [gmx-users] Energy minimisation problems - coordinate file and topology file not matching.

Yeah ... hadn't realised they were there when I began the simulating Natalie xxx From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: 22 September 2010 13:37 To: Discussion list for GROMAC

[gmx-users] REg QM/MM Mdrun error

Very very thank you sir; further when i run Mdrun after energy minimisatins by following command ./mdrun_d -s spep_em.tpr -o spep_em.trr -c spep_b4pr.gro -g em.log I got errror as follows i am using Mopac/gromacs intrface QM/MM calculation requested. there we go! Layer 0 nr of QM atoms 14 QMlevel:

[gmx-users] Re: gmx-users Digest, Vol 77, Issue 142

Why do you try to do MP2. Mopac will only allow semi-empirical methods. Though that does not seem to be the source of the error. Gerrit further when i run Mdrun after energy minimisatins by following command ./mdrun_d -s spep_em.tpr -o spep_em.trr -c spep_b4pr.gro -g em.log I got errror as fo

[gmx-users] reg QM/MM mdrun error

THAHNKS for your reply when  i trying with   AM1/STO-3Gi got error as follows Program mdrun_d, VERSION 4.0.7 Source code file: qmmm.c, line: 684 Fatal error: Semi-empirical QM only supported with Mopac is there is any installation problem in Mopac/gromacs?. i have

Re: [gmx-users] reg QM/MM mdrun error

Did you try to run a pure QM job using MOPAC as well as running a pure MD job using GROMACS? This might be a good start before trying to mix the two On 09/22/2010 04:25 PM, vidhya sankar wrote: THAHNKS for your reply when i trying with AM1/STO-3Gi got error as follows Program mdrun_d, VERSION

[gmx-users] pdb2gmx eats a bond

Hi all, i have built an .rtp entry for a molecule with 310 bonds, for the opls force field. For pdb2gmx i use the following command (version 4.0.7) *pdb2gmx -f CAT.pdb -o -p -ignh -ter* -ter is there because it is no protein, and use no C- and N-terminus (since there are none). Her one quest

Re: [gmx-users] pdb2gmx eats a bond

Thomas Schlesier wrote: Hi all, i have built an .rtp entry for a molecule with 310 bonds, for the opls force field. For pdb2gmx i use the following command (version 4.0.7) *pdb2gmx -f CAT.pdb -o -p -ignh -ter* -ter is there because it is no protein, and use no C- and N-terminus (since ther

[gmx-users] Issue with Atom Types/Charges/Mass when including ATP in gromos53.a6

Dear all, I want to run some simulations of a kinase with an ATP molecule using gromacs 4.5.1 with the gromos53a6.ff forcefield. To generate the .gro and .top files I am running pdb2gmx -v -f ATP.pdb -p initial.top -o initial.gro -ff gromos53a6 -water spc Now the generated topology file shows so

Re: [gmx-users] Tables with forcefield

On 21/09/10 20:45, Sai Pooja wrote: I wanted to change the interactions between the Protein and Solvent so I tried using tables with the potential function scaled by a constant value. I wanted to use this in combination with forcefield parameters (charmm). I changed the combination rule in the fo

[gmx-users] rotational correlation function

Hello, Imagine if the total correlation function of a protein could be factorized into rotational and internal portions: Ctot(t)=Crot(t)*Cint(t). With which commands I can calculate the Ctot(t) and with which I can get the Crot(t)? Does g_rotacf produce the Crot(t)? What does the g_rms -fit do? I a

[gmx-users] Re: pdb2gmx eats a bond

You are right, overlooked the line. And thanks for the idea with the short run, i'm happy with anything, so that i don't must look into more then 300 bonds. Greetings Thomas Thomas Schlesier wrote: Hi all, i have built an .rtp entry for a molecule with 310 bonds, for the opls force field. F

[gmx-users] Re: gmx-users Digest, Vol 77, Issue 138

Dear All, I'm not sure if this is a bug or not. I downloaded and installed the new version of Gromacs, and compiled it fine, and recompiled just mdrun_mpi The problem I now encounter. U was using 53a6 FF, which worked in the past, although I am partial to all atoms. In Pro residues, th

[gmx-users] Question about building and testing on imac

Hello, I built gromacs4.5.1 on my new imac (OS X 10.6.4) without problems using the command sequence: ./configure --enable-shared make make install Before that, I built fftw (3.2.2) by following the following sequence: ./configure --enable-threads --enable-float make make install However, mo

Re: [gmx-users] Question about building and testing on imac

Silvia Crivelli wrote: Hello, I built gromacs4.5.1 on my new imac (OS X 10.6.4) without problems using the command sequence: ./configure --enable-shared make make install Before that, I built fftw (3.2.2) by following the following sequence: ./configure --enable-threads --enable-float make

Re: [gmx-users] atomtype problem (was Re: gmx-users Digest, Vol 77, Issue 138)

I've gone ahead and changed the subject line to potentially attract the attention of others who might help. lloyd riggs wrote: Dear All, I'm not sure if this is a bug or not. I downloaded and installed the new version of Gromacs, and compiled it fine, and recompiled just mdrun_mpi The

Re: [gmx-users] Issue with Atom Types/Charges/Mass when including ATP in gromos53.a6

Hi, I am not sure why there is not an error message but something is going very wrong (from looking at the topology produced by pdb2gmx). I have had issues (in older versions of GROMACS) where the four letter naming of atoms for ATP in GROMOS has caused problems. I tried your pdb with the le

[gmx-users] rlist and rlistlong and grompp notes in gmx451

Dear Gromacs Users and Developers, I am testing gromacs-4.5.1 with different running parameters, in particular switching potentials and rlistlong, I have a question about this NOTEs: NOTE 1 [file qua.mdp]: For energy conservation with switch/shift potentials, rlist should be 0.1 to 0.3 nm lar

[gmx-users] Re: rotational correlation function

> Message: 2 > Date: Wed, 22 Sep 2010 12:07:27 -0600 > From: Paymon Pirzadeh > Subject: [gmx-users] rotational correlation function > To: gmx-users@gromacs.org > Message-ID: <1285178847.11669.66.ca...@paymon-desktop> > Content-Type: text/plain > > Hello, > Imagine if the total correlation function

Re: [gmx-users] Re: rotational correlation function

Dear Dr. Chaban, I meant the N-H bond vectors of protein backbone for calculation of rotational time correlation function to calculate the rotational diffusion constant of my protein. I need a protocol which walks me step by step through the procedure. Thanks for your Attention. Paymon On Wed, 2

Re: [gmx-users] Re: rotational correlation function

Hmm... Rotational time..? If you need diffusion constant, just use g_rotacf and then integrate the resulting VACF. If I recall correctly, you should make an index file with three numbers to define two vectors for the calculation. On Wed, Sep 22, 2010 at 7:27 PM, Paymon Pirzadeh wrote: > Dear Dr.

[gmx-users] Re: rotational correlation function

On Wed, Sep 22, 2010 at 7:47 PM, Paymon Pirzadeh wrote: > Well, I found a paper: J. Chem Phys. Vol. 131, 155103 (2009) in which > they have used GROMACS and its utilities to calculate the correlation > functions I need, however, it is not clear to me what utilities were > used and what steps were

Re: [gmx-users] Re: rotational correlation function

On 2010-09-23 01.27, Paymon Pirzadeh wrote: Dear Dr. Chaban, I meant the N-H bond vectors of protein backbone for calculation of rotational time correlation function to calculate the rotational diffusion constant of my protein. I need a protocol which walks me step by step through the procedure.