Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 136, Issue 133

Yes,I did, Mark. Thanks! But I don't need GTP. The pdb file just shows a GTP-binding site. So, how do I proceed? On Thu, Aug 27, 2015 at 2:52 PM, gromacs.org_gmx-users-requ...@maillist.sys.kth.se wrote: Send gromacs.org_gmx-users mailing list submissions to

Re: [gmx-users] OPLS forcefield amide charge

Hey, I myself am working on a polymer with an amide side chain, namely Polyacrylamide. I began my work picking up charges from the pre-defined Glutamine in the OPLS force-field. That amounted to a lot of time wasted as the density and glass transition temperature were a lot deviated from the

Re: [gmx-users] Fatal error: Residue 'GTP' not found in residue topology, database

Please heed this: When replying, please edit your Subject line so it is more specific than Re: Contents of gromacs.org_gmx-users digest... ...and don't reply to the entire digest. On 8/28/15 2:01 AM, Raag Saluja wrote: Yes,I did, Mark. Thanks! But I don't need GTP. The pdb file just shows

[gmx-users] trjcat problem

Dear all, I would like to concatenate different parts of my *.xtc files into one single file. But different parts have varying timesteps. Using trjcat I am getting following error: Reading frame 0 time0.000 # Atoms 273474 Precision 0.001 (nm) Reading frame 34000 time 68000.000

Re: [gmx-users] trjcat problem

Hi, That's not an error. It's just letting you know something that seems unusual that maybe you want to manage. Or ignore :-) Mark On Fri, Aug 28, 2015 at 3:34 PM pratibha kapoor kapoorpratib...@gmail.com wrote: Dear all, I would like to concatenate different parts of my *.xtc files into

Re: [gmx-users] Configuration bug preventing GROMACS 5.0 build with Intel compiler?

The newest Intel MPI, 5.1.1.109 at least, have fixed the bug with the wrappers. On 06/26/2015 03:51 PM, Mark Abraham wrote: Hi, I haven't tried to build with IntelMPI for a while, but we might consider patches to work around issues. Depends how ugly they make the things that are not broken

[gmx-users] REMD temperature trajectory

Dear Gromacs user, I performed a REMD simulation and I want to analyse my result per temperature. I am interested at looking the trajectory for the lowest and the highest temperature. I am used to perform REMD with Amber and I realised that Amber exchanges temperature during the

Re: [gmx-users] HREX simulation

The exchange attempt forces replicas to synchronize, and this forces the whole simulation system to pay the cost of any localized slow-down (e.g. network traffic congestion, internal simulation load imbalance from diffusion, even throttling of core clocks from heating effects) at each

Re: [gmx-users] g_chi Segmentation fault for -maxchi greater than 3

I found that with an older version g_chi works fine for the system. Thanks for your help. On Thu, Aug 27, 2015 at 9:15 PM, Dina Mirijanian dmi...@brandeis.edu wrote: No. I have ARG and LYS residues. And I checked the protein trajectory after trjconv and these residues seemed to be whole.

Re: [gmx-users] HREX simulation

Hi, On Fri, Aug 28, 2015 at 5:02 PM Michael Shirts mrshi...@gmail.com wrote: I am new to doing replica exchange simulations. I am trying to understand the empirical transition matrix printed in the log files. I tried exchange intervals 2 ps and 0.2 ps. However, later I read gromacs

Re: [gmx-users] g_chi Segmentation fault for -maxchi greater than 3

On 8/28/15 11:30 AM, Dina Mirijanian wrote: I found that with an older version g_chi works fine for the system. Thanks for your help. Then we clearly have a bug that needs to be fixed. If you would, please upload a test case (.tpr and a single coordinate file should do it) to

Re: [gmx-users] g_chi Segmentation fault for -maxchi greater than 3

OK. WIll do. For FYI here are the versions I tested and the version that worked: GROMACS/5.0.6NO GROMACS/5.0.5NO GROMACS/5.0.4NO GROMACS/4.6.3NO GROMACS/4.5.5YES! On Fri, Aug 28, 2015 at 11:33 AM, Justin Lemkul jalem...@vt.edu wrote: On 8/28/15 11:30

Re: [gmx-users] HREX simulation

I am new to doing replica exchange simulations. I am trying to understand the empirical transition matrix printed in the log files. I tried exchange intervals 2 ps and 0.2 ps. However, later I read gromacs recommends exchange interval not to be under 1ps. I don't know that there are firm

Re: [gmx-users] DPPC/DPPE minim.mdp

On 8/28/15 1:23 PM, Poncho Arvayo Zatarain wrote: Hello, i want to simulate a 128 DPPC molecule, 3655 water molecules but with 25% of DPPE. I replace de 25% of 128 DPPC molecules with DPPE and i'ḿ using the same forcefield and topology reported by Lemkul in his KALP15 in DPPC tutorial. When

Re: [gmx-users] OPLS forcefield amide charge

Hey. I am extremely sorry about the incorrect reference. I should have been careful. You should find the right charges in the supporting information of the following paper. http://www.ncbi.nlm.nih.gov/pubmed/22901375 Goodluck! Pallavi Banerjee. -- Gromacs Users mailing list * Please search

[gmx-users] DPPC/DPPE minim.mdp

Hello, i want to simulate a 128 DPPC molecule, 3655 water molecules but with 25% of DPPE. I replace de 25% of 128 DPPC molecules with DPPE and i'ḿ using the same forcefield and topology reported by Lemkul in his KALP15 in DPPC tutorial. When i want to minimize the energy i use the command

[gmx-users] Membrane simulation fatal error

Dear Gromacs Experts I am running a tutoriall for the membrane simulation, I found the following fatal error on running grompp command Fatal error: Atomtype CA not found my lipid.itp or ffnonbonded.itp do not contain the HW atom types or the lines like ;; parameters for lipid-GROMOS

Re: [gmx-users] OPLS forcefield amide charge

Thanks! On Fri, Aug 28, 2015 at 9:57 AM, Pallavi Banerjee pallavis...@students.iiserpune.ac.in wrote: Hey. I am extremely sorry about the incorrect reference. I should have been careful. You should find the right charges in the supporting information of the following paper.

Re: [gmx-users] Membrane simulation fatal error

On 8/28/15 2:11 PM, muhammad tahir ayub wrote: Dear Gromacs Experts I am running a tutoriall for the membrane simulation, I found the following fatal error on running grompp command Fatal error: Atomtype CA not found my lipid.itp or ffnonbonded.itp do not contain the HW atom types or the