[gmx-users] installing Gromacs4.6.3 with CPMD

Hallo everyone I would like to know if anyone has installed gromacs4.6.3 with CPMD, or how to monitor this installation? I couldn't find the installation procedure in the manual of gromacs4.6 I am looking forwards any suggestions. Thanks Collins -- gmx-users mailing listgmx-users@gromacs.o

[gmx-users] 1. Re: Interaction energy between specific residue in a set of residues (Justin Lemkul)

et of residues > To: Discussion list for GROMACS users > Message-ID: <51f97348.1010...@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > On 7/31/13 4:20 PM, Collins Nganou wrote: > > Dear all, > > > > I am looking how I can extrac

[gmx-users] Re: Interaction energy between specific residue in a set of residues

know how to ask make_ndx to read C5-C6 in DT with looking for the DA. Please If you can suggest me something it will be great for me. I wish you a wonderful day. Collins On Wed, Jul 31, 2013 at 4:20 PM, Collins Nganou wrote: > > Dear all, > > I am looking how I can extract the

[gmx-users] Interaction energy between specific residue in a set of residues

Dear all, I am looking how I can extract the interaction energy between specific residue in a set of residues. example: I have DT and DA residues, I would like to plot only the energy of the DT. I can extract the DT with the index file, But I am missing information on how to plot the energy b

[gmx-users] probabilty density of C5-C6 bond of all DNA conformer

Dear Users, I am looking the way to extract the probability density of the C5-C6. I will be very grateful to receive an indication on how to monitor it. Best regards Collins -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search th

[gmx-users] Re: gmx-users Digest, Vol 111, Issue 112

Lemkul) >2. interaction energy using g_enemat (Poojari, Chetan) >3. R: Re: [gmx-users] Rotation Constraints - PMF + rerun > (battis...@libero.it) > 4. Re: OpenSuse 12.1 + CUDA Installation Erro

[gmx-users] Index error

Dear Users, I would like to know if anyone may help me understand how to update the index file. I am trying to simulate a dna in solution. I have relaxed a Solvent with attached min.mdp file without problem. in the second step I was intended to relax SOL + Na DNA with 20ps.mdp. But the index file

[gmx-users] Re: gmx-users Digest, Vol 111, Issue 101

- > > Message: 1 > Date: Sun, 21 Jul 2013 07:14:30 -0400 > From: Justin Lemkul > Subject: Re: [gmx-users] mdrun error > To: Discussion list for GROMACS users > Message-ID: <51ebc296.1080...@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > &

[gmx-users] mdrun error

Dear Users, when trying to run the following command: mdrun -v -deffnm protein-EM-solvated -c protein-EM-solvated.pdb I have received the error below. Reading file dna-EM-solvated.tpr, VERSION 4.5.5 (single precision) Starting 2 threads --- P

[gmx-users] Save all MD snapshot

Dear Users. Greetings. Please someone can tell me how can I proceed to save all MD snapshot for a long time simulation after equilibration. Thanks a lot for all. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo

[gmx-users] Analyse of velocity autocorrelation function plot by xmgrace

Dear gmx-users, Greetings. As I receive advice, I already plot velocity autocorrelation with xmgrace. the file is attached. As you see in this file, it is not possible for my to do distinction between noise and movement in this plot. Someone can explain me what can I do ? Many thanks. vac_

[gmx-users] cumulative velocity correlation

Dear gmx-Users, Greetings. Please someone can tell me how to run cumulative velocity correlation with gromacs and perform Fourier spectral analysis of the cumulative velocity correlation function Thanks to all response. __

[gmx-users] Hessian matrix calculation

Dear Users. Greetings. I want the perform hessian matrix with mdrun by option -mtx nm.mtx, But I didn't receive a out put nm.mtx I run this command after minimization of my structure. Can you help me to understand why mdrun didn't give me a output nm.mtx for Hessian but only traj.trr.

[gmx-users] Choose of force fields of ethanol and B-DNA with 15 base pairs

Dear all. greetings. I need to know what force fields can I Choose to run: 1- ethanol vibrational mode. 2- B-DNA with 15 base pairs Thanks a lot for the response ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listin

[gmx-users] MTH force field

Dear all. Please, How can I do to have MTH this force field. MTH ffgmx.rtp - methanolCH3OH Thanks a lot ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the arch

[gmx-users] CO2.pdb

Dear gmx-users, Greetings. I try to have methane pdb. or CO2.pdb to understand basically how to have a vibrational mode. But I have problem with imput pbd file. ATOM 1 C1METH1 3.875 0.678 -8.417 1.00 0.00 ATOM 2 H1 METH1 3.800 1.690 -8.076 1.00 0.

[gmx-users] Re: gmx-users Digest, Vol 48, Issue 9

Dear all greeting I am a new user in gromacs . To begin, I need to know how to generate date for simple water molecule and observe vibrational modes. I use this command as well as read in the manual: pdb2gmx -f prot.pdb -o prot.gro -p prot.top but when I choose ff 43a1 Opening library file /usr/