[gmx-users] .mdp file

Hey hi i want to do gromacs tutorial and for that i required the .mdp file for where i can get that file and what type of modification should i do in that file With Best Regards. Mr.Manoj Damale, M.S. Pharma (Pharmacoinformatics) NIPER, Kolkata, West Bengal State, India.-- gmx-users mailin

Re: [gmx-users] .mdp file

On 9/08/2011 5:26 PM, manoj damale wrote: Hey hi i want to do gromacs tutorial and for that i required the .mdp file for where i can get that file The tutorial will tell you how to get it or create it. and what type of modification should i do in that file Whatever the tutorial suggests

Re: [gmx-users] .mdp file

Dear Mark, Excellent suggestion, i'll also follow it to be a good gromacs user. Perhaps reading books, literature, searching on-line resources, go through tutorial or manual is always evergreen idea, but a bit hard work needed (To be an expert). Thanks a lot. Best Regards sharma On T

[gmx-users] Contribution of delta bonding energy in the delta free energy

Hi, I used thermodynamics integration method (TI) to obtain delta Gibbs energy of the protein membrane. I want to separate contributions of delta bonding and nonbonding energy in delta Gibbs energy. Best wishes, Maleki, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs

[gmx-users] Obtain in a readable format the pairtypes values generated by grompp

Dear All, For verification purposes, I would like to obtain in a readable format the list of the pairtypes values for a molecule generated by grompp when the gen-pairs directive is set to "yes" in forcefield.itp file. It is possible ? If yes, how? Thank you in advance for your response

Re: [gmx-users] Contribution of delta bonding energy in the delta free energy

On 9/08/2011 9:13 PM, afsaneh maleki wrote: Hi, I used thermodynamics integration method (TI) to obtain delta Gibbs energy of the protein membrane. I want to separate contributions of delta bonding and nonbonding energy in delta Gibbs energy. So instead of using the sum of bonded and non-

Re: [gmx-users] Obtain in a readable format the pairtypes values generated by grompp

On 9/08/2011 10:23 PM, intra\sa175950 wrote: Dear All, For verification purposes, I would like to obtain in a readable format the list of the pairtypes values for a molecule generated by grompp when the gen-pairs directive is set to "yes" in forcefield.itp file. It is possible ? If yes, how

[gmx-users] git release-4-5-patches behind proxy

I want to calculate secondary structure propensities of residues. Following Mark's message on thread Re: [gmx-users] secondary structure propensities of residues I would like to get the release-4.5-patches from git (in order to get do_dssp.c). Nevertheless I found problems while trying to fetch

[gmx-users] RE: gmx-users Digest, Vol 88, Issue 46

gt; Thank you in advance for your response > > Stephane > > > -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20110809/53fb7878/a ttachment-0001.html -- Message: 5 Date:

[gmx-users] LINCS with amber99SB ?

Hi all, I want to do MD simulation with amber99SB force field, which I found originally developed using SHAKE algorithm to constrain all bonds involving hydrogen atoms. But it seems to me that SHAKE is still not supported with domain decomposition in GROMACS4.5.4, and we can only use LINCS for bon

[gmx-users] TR: Obtain in a readable format the pairtypes values generated by grompp

Thank you Mark for the commands. It is indeed what I want. Stephane > On 9/08/2011 10:23 PM, intra\sa175950 wrote: > > > > Dear All, > > > > For verification purposes, I would like to obtain in a readable format > > the list of the pairtypes values for a molecule generated by grompp > > when th

Re: [gmx-users] git release-4-5-patches behind proxy

Hi, please try "git pull" (for repo.or.cz) and than redo the checkout. I accidentally deleted the release-4-5-patches branch. But it is back and it should work. If it does not work please run "git branch -r" and post the result. BTW: The error message you get for git.gromacs.org suggests that you

Re: [gmx-users] LINCS with amber99SB ?

Yun Shi wrote: Hi all, I want to do MD simulation with amber99SB force field, which I found originally developed using SHAKE algorithm to constrain all bonds involving hydrogen atoms. But it seems to me that SHAKE is still not supported with domain decomposition in GROMACS4.5.4, and we can

[gmx-users] Force evaluation in umbrella pulling with nonzero pull_rate

Hi, I'm trying to use umbrella pulling to do a targeted MD and I have the following pull code: pull= umbrella pull_geometry = distance pull_dim= N N Y pull_start = no pull_ngroups = 1 pull_group0 = REF pull_group1 = PULL pull_init1

[gmx-users] Re: Free energy calculation

Thanks Justin. Best regards, Fabian On Mon, Aug 8, 2011 at 5:49 PM, Fabian Casteblanco wrote: > Hello all, > > I am setting up a free energy calculation (drug from full coulomb+vdW > in solution --> drug with only vdW in solution --> dummy drug in > solution). > > After reading most of the paper

[gmx-users] Gromacs compilation

Dear User: I compiled GROMACS with OPEN64 without problems, Now I want to compile it using the ACML libraries to compare the performance How I can compile gromacs using the ACML libraries? I tried: ./configure CC=opencc CXX=openCC F77=openf90 CFLAGS="-O3 -OPT:Ofast -march=barcelona -LGROMACS_SUI

[gmx-users] Invitation to connect on LinkedIn

LinkedIn MING LI requested to add you as a connection on LinkedIn: -- Chinmay, I'd like to add you to my professional network on LinkedIn. - MING Accept invitation from MING LI http://www.linkedin.com/e/-85v1n9-gr58nre7-5n/Xl9gjr6G

[gmx-users] Invitation to connect on LinkedIn

LinkedIn MING LI requested to add you as a connection on LinkedIn: -- Chinmay, I'd like to add you to my professional network on LinkedIn. - MING Accept invitation from MING LI http://www.linkedin.com/e/-85v1n9-gr58q7r2-6w/Xl9gjr6G

Re: [gmx-users] secondary structure propensities of residues

Hi, I downloaded release-4-5-patches from git. It compiles and installs successfully. Nevertheless I am getting a segmentation fault. With gdb I am getting the following messages gdb --args do_dssp -f ../0_trajout.xtc -s ../input/replica_0.tpr -ssdump data.dat -b 17 -e 18 -dt 10 GNU gdb (

Re: [gmx-users] Contribution of delta bonding energy in the delta free energy

Dear Mark, I used thermodynamics integration method (TI) to obtain delta Gibbs energy of the protein membrane with dual topology. topology A (lambda=0) to topology B (lambda=1) What i obtained after using mdrun command to calculate free energy is dgdl.xvg that contain dV(total)/dlamda via time. I

[gmx-users] Re: LINCS with amber99SB ?

Thank you for the reply. Just to clarify. In the original gromos 53a6 paper, all bonds were constrained, while in amber99sb paper only bonds involving H atoms were constrained. So as long as I stick to the same groups of bonds constrained as in the development of respective forcefields, it is alwa

Re: [gmx-users] Contribution of delta bonding energy in the delta free energy

afsaneh maleki wrote: Dear Mark, I used thermodynamics integration method (TI) to obtain delta Gibbs energy of the protein membrane with dual topology. topology A (lambda=0) to topology B (lambda=1) What did you alter between these two topologies? Nonbonded terms (atom types and/or ch

Re: [gmx-users] Re: LINCS with amber99SB ?

Yun Shi wrote: Thank you for the reply. Just to clarify. In the original gromos 53a6 paper, all bonds were constrained, while in amber99sb paper only bonds involving H atoms were constrained. So as long as I stick to the same groups of bonds constrained as in the development of respective f

[gmx-users] Regarding PCA and Gibbs Free energy landscape

Hello, I have done PCA using cartesian coordinates by the help of gromacs(g_covar and g_anaeig), then using the 2-d projection of trajectory on first two eigenvectors as reaction coordinates,I have calculated a 2-d representation of the gibbs free energy landscape using gromacs.Now on this landscap

[gmx-users] VMD_PLUGIN_PATH

Hi Gromacs Users, I am using the gromacs analysing tools to analyze my DCD file produced by NAMD. I set up the VMD_PLUGIN_PATH before running however I got the error that the VMD_PLUGIN_PATH was not set up. Can anyone give me a hand? Please see below the details. Thanks for the help export VMD_PL

[gmx-users] Regarding Equilibration

Dear all, Could you please tell me what kind of error limit is accepted for running NVT and NPT equilibration in terms of Temperature, Pressure and Density. Thank you, With Regards, Ravi Kumar V IPC Dept., IISc, INDIA. -- gmx-users mailing listgmx-users@gromacs.org http://lists