Re: [gmx-users] Getting started - Peptide

Hi All, Thank you very much for suggestions! It turned out that there was a missing entry in the top file. After adding the following: #include "spc.itp" grommp finished without any errors :-) Cheers, Artur 2010/9/23 TJ Mustard : > On September 23, 2010 at 3:02 PM Artur Panczakiewicz > wrote:

Re: Re: [gmx-users] Issue with Atom Types/Charges/Mass when

Dear Tom, I know that there were some ATP-related issues in past versions of gromacs using the gromos-ff: Gromos used some 5-letter atom types which was a problem as the pdb file format only has 4 columns for them so you had to do some renaming. I thought this not to be an issue anymore and am sur

[gmx-users] Reg: Putting molecules on one side of the box

Hi all I have a triclinic box of length of 8*3*3 nm. i want to put water on one side of the box and say decane on the other side of the box. How to generate .gro for the water-decane mixture such that they form two distinct parts of the box. Regards Vinoth -- gmx-users mailing listgmx-users@

[gmx-users] fftw and configure in 4.0.7 vs 4.5.1

Hi everybody, I'm experiencing several problems by running configure in 4.5.1. More specifically, it seems it doesn't find fftw libraries. It seems strange 'cause the same options used in 4.0.7 work fine. These are my configure flags: ./configure --prefix=/bgp/userinternal/cin0644a/gromacs \

Re: [gmx-users] Getting started - Peptide

Hi All, Thank you very much for suggestions! It turned out that there was a missing entry in the top file. After adding the following: #include "spc.itp" grommp finished without any errors :-) Cheers, Artur 2010/9/23 TJ Mustard : > On September 23, 2010 at 3:02 PM Artur Panczakiewicz > wrote: >

Re: [gmx-users] fftw and configure in 4.0.7 vs 4.5.1

- Original Message - From: Fabio Affinito Date: Friday, September 24, 2010 17:23 Subject: [gmx-users] fftw and configure in 4.0.7 vs 4.5.1 To: gmx-users@gromacs.org > Hi everybody, > I'm experiencing several problems by running configure in 4.5.1. More > specifically, it seems it doesn'

[gmx-users] PMF on dihedral

Landry, I replied earlier, but it didn't seem to make it to the list. If 2 show up then they are identical. The mailing list archive post that you cite is actually talking about a (3-point) angle and not a (4-point) dihedral angle. If you want dihedral angles, then take a look at how w

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

OK, To summurize: 1. I calculate the Ctot(t) with g_rotacf using N-H index files. 2. Use trjconv to get a trajectory of internal motions. => How I get the Cint(t)??? 3. Crot = Ctot/Cint But, is there any way to calculate the Crot(t) directly? Is trjconv the solution again? regards, Paymo

Re: [gmx-users] ffyw3f library not found..

Hi Mark, thanks for the explanation. Anyway, I had this kind of problem only when configuring for the frontend, whilst everything was ok with fftw3 when I configured and compiled for the computation nodes. Fabio On 09/23/2010 03:20 PM, Mark Abraham wrote: > > > - Original Message - > Fr

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

On 2010-09-23 21.10, Paymon Pirzadeh wrote: OK, To summurize: 1. I calculate the Ctot(t) with g_rotacf using N-H index files. 2. Use trjconv to get a trajectory of internal motions. => How I get the Cint(t)??? 3. Crot = Ctot/Cint But, is there any way to calculate the Crot(t) directly?

[gmx-users] make_ndx: execlude one group from another

Hi all, I'm trying to execlude all atoms of group 2 (140 atoms) from group 1 (300 atoms), so that i have a new group 3 (with 160 atoms). | is for merging with OR & for merging with AND so ! should be for merging with NOT But i tried 1 ! 2 2 ! 1 but in both cases make_ndx complains about syntax e

[gmx-users] trouble in energy minimization.

Hi, I used gromacs package (ver 4.0.3) for energy minimization of protein homology model.After em, some residues were mangled if I see structure using jV protein structure view (http://www.pdbj.org/jv/index.html) and rasmol.Especially, some glycine were disappeared on jV viewer and rasmol. It maybe

[gmx-users] D-proline

Dear Gromacs users, I would like to use gromacs to simulate a peptide containing a D-proline using the opls force field. I guess that, considering that L- and D- PRO differs only for chirality, the two a.a. topologies should little differ, and that an improper torsion and/or torsional terms

Re: [gmx-users] make_ndx: execlude one group from another

Thomas Schlesier skrev 2010-09-23 13.03: Hi all, I'm trying to execlude all atoms of group 2 (140 atoms) from group 1 (300 atoms), so that i have a new group 3 (with 160 atoms). | is for merging with OR & for merging with AND so ! should be for merging with NOT But i tried 1 ! 2 2 ! 1 but in b

Re: [gmx-users] ffyw3f library not found..

Kamalesh Roy wrote: Thanks for your answer. I have given the command ./configure then make then make install for fftw and then ./configure for gromacs then it returns a command that fftwf library not found. I kept the fftw and gromacs file in the same directory /usr/local and was trying to

Re: [gmx-users] Reg: Putting molecules on one side of the box

Use genconf to replicate some suitable smaller box of decane to the full size, delete the second half of the decane molecules, then use genbox to fill the rest with water. Cunning use of genconf should allow you to select where the division lies. Mark - Original Message - From: vinothk

[gmx-users] Re: Problem with pressure coupling

And I have just noticed that this was an mdp after some testing with changed values. It behaves the same also with the more sensible values below. Moreover, it looks like something that will not be sensitive to the details of the the FF evaluation. rlist= 1.2 rcoulomb-switch

[gmx-users] PMF on dihedral

Landry, you can't do it using the pull code, but it is possible. We did US over Phi and Psi in the following paper, and you can get the methods from there. I also posted many more specifics and examples to the mailing list during that time. C. Neale, T. Rodinger, and R. Pomès, "Equi

Re: [gmx-users] make_ndx: execlude one group from another

- Original Message - From: Thomas Schlesier Date: Friday, September 24, 2010 18:43 Subject: [gmx-users] make_ndx: execlude one group from another To: "gmx-users@gromacs.org" > Hi all, > I'm trying to execlude all atoms of group 2 (140 atoms) from > group 1 (300 atoms), so that i have

[gmx-users] Re: gmx-users Digest, Vol 77, Issue 150

Dear Users and Justin, Included below is the origional message and reply. The only error message was " Atom type CH2r not found fatal error ". After looking at all the files though, I realized if I change everything to either CH2r or CH2R , it runs. I don't know if it was somones joke on my

RE: [gmx-users] Getting started - Peptide

Are you sure you installed the version 4.0.7? Hint : your program run on VERSION 4.5.1, Answer : You know. lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Artur Panczakiewicz [apanczakiew...@gmail.com] Sent: Thursd

[gmx-users] make_ndx: execlude one group from another

Hi all, I'm trying to execlude all atoms of group 2 (140 atoms) from group 1 (300 atoms), so that i have a new group 3 (with 160 atoms). | is for merging with OR & for merging with AND so ! should be for merging with NOT But i tried 1 ! 2 2 ! 1 but in both cases make_ndx complains about syntax e

Re: [gmx-users] ffyw3f library not found..

Thanks for your answer. I have given the command ./configure then make then make install for fftw and then ./configure for gromacs then it returns a command that fftwf library not found. I kept the fftw and gromacs file in the same directory /usr/local and was trying to install this. Thank you

Re: [gmx-users] Getting started - Peptide

Artur Panczakiewicz wrote: Dear Gromacs Users, I'm a freshman and would like to lear how to use GROMACS in my research starting from tutorial. I've just installed the newest version and try to repeat all of the steps from the chapter that describes the preparation of Ribonuclease A to MD simul

Re: [gmx-users] atomtype problem (was Re: gmx-users Digest, Vol 77, Issue 150)

lloyd riggs wrote: Dear Users and Justin, Included below is the origional message and reply. The only error message was " Atom type CH2r not found fatal error ". After looking at all the files though, I realized if I change everything to either CH2r or CH2R , it runs. I don't know if it wa

[gmx-users] Getting started - Peptide

Dear Gromacs Users, I'm a freshman and would like to lear how to use GROMACS in my research starting from tutorial. I've just installed the newest version and try to repeat all of the steps from the chapter that describes the preparation of Ribonuclease A to MD simulation. In my case it is not pos

Re: [gmx-users] ffyw3f library not found..

- Original Message - From: Kamalesh Roy Date: Friday, September 24, 2010 21:36 Subject: Re: [gmx-users] ffyw3f library not found.. To: jalem...@vt.edu, Discussion list for GROMACS users > Thanks for your answer. > I have given the command ./configure then make then make install for fft

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

Dear Timo Thank you for your reply.  i successfullly run pure mopac7-1.11 and Pure MD in gromacs as u said  but still got same  error when i run QM/MM mopac/gromacs interface as follollows   when i trying with AM1/STO-3Gi got error as follows > Program mdrun_d, VERSION 4.0.7 > Source code file:

[gmx-users] Problem with pressure coupling

Dear all, running a box of neat water with the below mdp file in GROMACS 4.5.1 results in a fast linear increase of the volume of the box, the water getting torn into clusters. The same simulation in 4.0.7 (with nstcalcenergy removed, of course) runs just fine, with the box volume stable and fluct

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

There is a page on how to compile mopac and gromacs to enable qm/mm simulations: http://www.gromacs.org/index.php?title=Download_%26_Installation/Installation_Instructions/compiling_QMMM as you seem to have all the dependencies now(?), you will have to modify and compile both mopac, as well as g

[gmx-users] CHARMM -> gromacs epsilon and sigma conversiion factors

Hi all, I would like to add new atom types in the charmm27.ff for futures simulations of glyolipids in water with gmx 4.5.1. I have finished to convert the bonded in GROMACS format. However, I am little puzzled with the vdW paramaters. I would like to know how to convert them (i.e. what are t

Re: [gmx-users] D-proline

On Fri, Sep 24, 2010 at 03:28, Stefano Pieraccini wrote: > I would like to use gromacs to simulate a peptide containing a D-proline > using the opls force field. I guess that, considering that L- and D- PRO > differs only for chirality, the two a.a. topologies should little differ, > and that an i

Re: [gmx-users] Tables with forcefield

Hi, Clarifications inline... On Wed, Sep 22, 2010 at 2:01 PM, ms wrote: > 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

Re: [gmx-users] D-proline

Hi Stefano, Using C N CA CD instead of C CA N C inverts the improper dihedral. And unlike all atom force fields, you can start from an L-proline :) Cheers, Tsjerk On Sep 24, 2010 10:46 AM, "Stefano Pieraccini" wrote: Dear Gromacs users, I would like to use gromacs to simulate a peptide

[gmx-users] MPI

Hi, This is the same email that I'd sent yesterday but has not got posted? Hi, I have some questions about installation of GROMACS with MPI. Our system administrator has installed the 4.5.1 version in our system. When I tested the software with "openmpi/openmpi-1.3.3-gcc/bin/mpirun" with mdrun_mpi,

Re: [gmx-users] MPI

Guess my reply never hit the list, either, but it's in the archive: http://lists.gromacs.org/pipermail/gmx-users/2010-September/054259.html -Justin simon sham wrote: Hi, This is the same email that I'd sent yesterday but has not got posted? Hi, I have some questions about installation of GROM

[gmx-users] vanadium non-bonded parameters

Dear gmx'ers, Does anyone know of any (published or not) non-bonded parameters for vanadium species for any of the forcefields implemented in GROMACS ? If not, my question is: what is the meaning of the null values for sigma and epsilon in, e.g., amber03, for Fe: FE 26 55.000.0

[gmx-users] CHARMM -> gromacs epsilon and sigma conversiion

eps(charmm)*4.184=epsilon(Gromacs) 0.15*4.184=0.6276 Rmin/2(Charmm)*2/(2^1/6)=sigma(Gromacs) 2.27*2/(2^(1/6))=0.404468(nm) Cheers, Jianhui Date: Fri, 24 Sep 2010 15:55:44 +0200 From: "ABEL Stephane 175950" Subject: [gmx-users] CHARMM -> gromacs epsilon and sigma conversiion factors To:

Re: [gmx-users] vanadium non-bonded parameters

Hi Gonçalo If you do not find the parameters for vanadium, you could try to develop them using experimental physical chemistry properties of the ion and MD simulations. In the following reference you can find a suitable method to develop them that worked for me in the development of Pb and Cd

[gmx-users] data.xvg for g_kinetics ?

Hi gromacs user, We recently ran in this problem when try to analyise our REMD trajectories. g_kinetics module will be used for such kinda analysis, however it looks like we need provide 2 xvgs file as input. The temp.xvg we can get from demux.pl and the other one (data.xvg) we are not sure how

[gmx-users] local pressure

Hi all, Is it possible to compute local pressure in gromacs (e.g. according to Hoover et al., 1991)? Thanks in advance. -- Dr. Vitaly V. Chaban Department of Chemistry University of Rochester Rochester, NY 14627-0216 United States of America -- gmx-users mailing listgmx-users@gromacs.org h

Re: [gmx-users] data.xvg for g_kinetics ?

feng chen wrote: Hi gromacs user, We recently ran in this problem when try to analyise our REMD trajectories. g_kinetics module will be used for such kinda analysis, however it looks like we need provide 2 xvgs file as input. The temp.xvg we can get from demux.pl and t

[gmx-users] Re: MPI

--- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20100924/2a671694/attachment-0001.html -- Message: 3 Date: Fri, 24 Sep 2010 15:18:27 -0400 From: "Justin A. Lemkul" Subject: Re: [gmx-users] MPI To: Discu

Re: [gmx-users] Re: MPI

n I configure the software with openmpi? Thanks for your help in advance. Best, Simon Sham -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20100924

Re: [gmx-users] Tables with forcefield

Hi, Clarification: I may not be able to help you directly but I can suggest you which information you should perhaps give us to enable people more knowledgeable than me to help. On 24/09/10 17:33, Sai Pooja wrote: I use combination rule 1; but I also define all tabulated interactions for all