[gmx-users] Tc grps, one group or two?

Dear all, I have doubts that whether I should use two groups to control the temperature or just one since there are just 604 hundred Protein beads and 6+ solvent beads. It is said that two groups are more accurate but when when i split them into two groups Protein nonProtein, I found

Re: [gmx-users] C36 cyclopropanated lipids in Gromacs

On 6/11/14, 5:14 AM, Ariel Leong wrote: Hi, I'm interested to simulate lipids with cyclopropanated chains with Gromacs. The C36 parameters for the lipids have been publicly provided by Klauda et al. in CHARMM str format. I've looked at the C36 force field for Gromacs and it seems that they

[gmx-users] virtual site independent from other structure

Hello everyone, I would like to create a virtual site which is independent from other structure. Is this possible? Best regards, Linlin Sun -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post?

[gmx-users] GROMOS96 user guide

Dear Gromacs Users, Does anyone know where i can get 'GROMOS96 manual and user guide'(van Gunsteren, W. F.; Billeter, S. R.; Eising, A. A.; Hünenberger, P. H.; Krüger, P.; Mark, A. E.; Scott, W. R. P.; Tironi, I. G. Biomolecular Simulation: The GROMOS96 Manual and User Guide; vdf

Re: [gmx-users] C36 cyclopropanated lipids in Gromacs

Thank you, Justin. I've checked that out as well, but it was also missing the bacterial lipids containing cyclic moieties. On Wed, Jun 11, 2014 at 5:27 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/11/14, 5:14 AM, Ariel Leong wrote: Hi, I'm interested to simulate lipids with

Re: [gmx-users] C36 cyclopropanated lipids in Gromacs

On 6/11/14, 5:45 AM, Ariel Leong wrote: Thank you, Justin. I've checked that out as well, but it was also missing the bacterial lipids containing cyclic moieties. Those can easily be added using our stream file converter on the same page. I'll look into adding them as standard in a future

Re: [gmx-users] GROMOS96 user guide

On 6/11/14, 5:40 AM, Negar Parvizi wrote: Dear Gromacs Users, Does anyone know where i can get 'GROMOS96 manual and user guide'(van Gunsteren, W. F.; Billeter, S. R.; Eising, A. A.; Hünenberger, P. H.; Krüger, P.; Mark, A. E.; Scott, W. R. P.; Tironi, I. G. Biomolecular Simulation: The

Re: [gmx-users] virtual site independent from other structure

On 6/11/14, 5:39 AM, Linlin Sun wrote: Hello everyone, I would like to create a virtual site which is independent from other structure. Is this possible? No, virtual sites in Gromacs are always constructed relative to some defined atoms. -Justin --

Re: [gmx-users] C36 cyclopropanated lipids in Gromacs

Thanks for the suggestion, I'll have a try at the converter. On Wed, Jun 11, 2014 at 5:47 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/11/14, 5:45 AM, Ariel Leong wrote: Thank you, Justin. I've checked that out as well, but it was also missing the bacterial lipids containing cyclic

Re: [gmx-users] GROMOS96 user guide

You can look at preview versions of some of the chapters from the GROMOS manual on the ATB website: http://compbio.biosci.uq.edu.au/atb/index.py?tab=forceField_tabnocache=752 Cheers Tom From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se

Re: [gmx-users] Regarding membrane construction

Dear Justin, I am following membrane-protein tutorial to construct my system. During equilibration and production MD, I am receiving the following NOTES. NOTE 1 [file md.mdp]: nstcomm nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy NOTE 2 [file md.mdp]:

Re: [gmx-users] Regarding membrane construction

On 6/11/14, 6:25 AM, Venkat Reddy wrote: Dear Justin, I am following membrane-protein tutorial to construct my system. During equilibration and production MD, I am receiving the following NOTES. NOTE 1 [file md.mdp]: nstcomm nstcalcenergy defeats the purpose of nstcalcenergy, setting

Re: [gmx-users] hardware problem of GPU?

Hello Mark: I contact with my GPU workstation supplier and they said the following: As mentioned we did all the hardware settings to enable SLI: 1)The graphiccards are connected with the SLI bridge. 2)Additionaly the SLI settings have to be configured in the Nvidia driver as follows:

Re: [gmx-users] hardware problem of GPU?

This is not a hardware issue. See http://www.gromacs.org/Documentation/Acceleration_and_parallelization#Heterogenous_parallelization.3a_using_GPUs Mark On Wed, Jun 11, 2014 at 1:09 PM, Albert mailmd2...@gmail.com wrote: Hello Mark: I contact with my GPU workstation supplier and they said

[gmx-users] Broken molecule across periodic boundary: The sum of the two largest charge group radii (xxx) is larger than rlist (xxx)

Hi there, I understand this is an old issue, but no one seems to have a solution? So I want to take a snapshot from the middle of a MD trajectory (like 67ns point from a 100ns trajectory), preferably with all solvent molecules (waters and ions). However, after using trjconv -pbc to make

[gmx-users] Interaction energy between helices

Dear Gromacs users, I want to calculate the energy of interaction between two helices of a protein, but g_energy dont have the option for -ndx file to select these specific residues of a helix. How I can do this? Thanks for your suggestions! -- Natalia Alveal Fuentealba Ingeniera en

[gmx-users] Tc grps, one group or two?

Dear gromacs users, I have doubts that whether I should use two groups to control the temperature or just one since there are just 604 hundred Protein beads and 6+ solvent beads. It is said that two groups are more accurate but when when i split them into two groups Protein nonProtein,

Re: [gmx-users] Using specbond.dat in pdb2gmx

On 6/11/14, 2:33 PM, Matthew Stancea wrote: ? Hello, I have been having a bit of issues generating an accurate gromacs topology file (topol.top) utilizing a pdb of a cyclic peptide in pdb2gmx. I have been able to generate topologies that are almost identical to the original pdb using the

Re: [gmx-users] -inf potential with TPIC

I mistyped amber, when I should have typed charmm, amber is totally uninvolved in my calculations. I used the script from http://www.gromacs.org/Downloads/User_contributions/Other_software titled charmm2gromacs. The output looked fine after running it. And, I doubt its the cofactor, just ran