Re: [gmx-users] Environmental variable setting for gmx 5.0.4

On 04/01/2015 10:20 AM, yoochan wrote: Hi RJ, I think you need to inscribe 'source command' in your bash file. In case of Ubuntu environment, If you insert 'source command' for /etc/bash.bashrc, you can do use gromacs in all terminals without typing source command. This would affect

Re: [gmx-users] Environmental variable setting for gmx 5.0.4

Hi RJ, I think you need to inscribe 'source command' in your bash file. In case of Ubuntu environment, If you insert 'source command' for /etc/bash.bashrc, you can do use gromacs in all terminals without typing source command. You don’t need to set your PATH as you mentioned earlier.

[gmx-users] Temperature in Non-equilibrium MD simulation.

Dear all, As far as I understand GROMACS did NOT exclude the streaming velocity (Poisseuille flow) from the temperature calculation and I think it is not correct. I was wondering if someone has modified Gromacs code to obtain a good thermostat. Please let me know. Thank you very much. Tuan.

[gmx-users] ATB

Dear All Does the type of chemical bond (single, double, triple), built by JSME Molecular Editor, directly influence on the final results of Automated Topology Builder (http://compbio.biosci.uq.edu.au/atb/ ), not by number of built protons? I built a molecule with a some double bond, number of

Re: [gmx-users] Temperature in Non-equilibrium MD simulation.

Does the speed of your flows have comparable scale as the speed of sound? If very less, don't worry about temperature. On Wed, Apr 1, 2015 at 6:10 AM, Ho, Tuan A. tua...@ou.edu wrote: Dear all, As far as I understand GROMACS did NOT exclude the streaming velocity (Poisseuille flow) from the

[gmx-users] Fluorine Gromos LJ parameters

Hi, I've done an extensively search out the web but I could not find LJ parameters for Fluoride (ionic). Gromos54A7 has only Fluorine parameters. Does anyone knows any new parameters for that? Best regards! -- Marcelo Depólo Polêto Student of MSc Cell and Molecular Biology - UFRGS (Brazil)

[gmx-users] The largest charge group contains [GIANT CRAPTON] of atoms

I have a custom-FF (OPLSAA based) system with ~8500 atoms, which is a rectangular graphene sheet with a hole and six pieces of small organics covalently bound at the hole edge. About 95% of all atoms are electrically neutral, with the exception of the functional groups mentioned above and a total

[gmx-users] Gromacs running on single PC with GPU?

Dear gmx I have PC has 16 processor with GTX460 where i complied successfully by following the gmx procedure. When i run gmx mdrun, it does detects my gpu but i wonder whether its taking for calculation or not ? Here i get this info while running mdrun Using 1 MPI thread Using 16 OpenMP

Re: [gmx-users] Gromacs running on single PC with GPU?

On 02/04/2015 6:11 am, RJ ra...@kaist.ac.kr wrote: Dear gmx I have PC has 16 processor with GTX460 where i complied successfully by following the gmx procedure. When i run gmx mdrun, it does detects my gpu but i wonder whether its taking for calculation or not ? Here i get this info while

Re: [gmx-users] Environmental variable setting for gmx 5.0.4

Thanks a lot for your info Peter and Yoochan, Adding the source in /etc/bash.bashrc works in ubuntu. But I tried many times adding in ~/.bashrc before but it never worked to me. How do i deal wiith centos ? it doesnt have /etc/bash.bashrc file. I also added in ~/.bashrc but it doesnt work.

Re: [gmx-users] Environmental variable setting for gmx 5.0.4

Hi, Google is a good place to seek the answer for you shell and distribution - sounds like on centos you are not actually using bash! Mark On 02/04/2015 4:03 am, RJ ra...@kaist.ac.kr wrote: Thanks a lot for your info Peter and Yoochan, Adding the source in /etc/bash.bashrc works in ubuntu.

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 131, Issue 130

Hi, If you're opting for the convenience of recieving the digest, please consider that replying to it makes it impossible for people to follow the discussion unless you change the email subject to something useful. In turn, that might make it slower to get help ;-) On Wed, Apr 1, 2015 at 6:39

[gmx-users] simulate a multimer with one component has covalently attached prosthetic group

Hi all, I am trying to simulate a dimer (say A2) where another protein is docked (say B) which is covalently attached with a prosthetic group. My question is how to do that. so far what i did ... I generate a gro and itp file from PRODRG corresponding to that molecule and modified the

Re: [gmx-users] Partial Energy from Traj

Hi, You can use trjconv to get that subset from your trajectory, match it to a .tpr and then use the ideas at http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy Mark On Wed, Apr 1, 2015 at 6:08 PM, xy21hb xy2...@163.com wrote: Dear all, I have a simple protein-in-water binary

[gmx-users] Automated Topology Builder

Does the type of chemical bond (single, double, triple), built by JSME Molecular Editor, directly influence on the final result of Automated Topology Builder (http://compbio.biosci.uq.edu.au/atb/

[gmx-users] grompp: unknown bond_atomtype

I am working with a local copy of oplsaa.ff where I have defined a set of custom atom types in atomname2type.n2t and added the bond and angle parameters into ffbonded. x2top creates the topology without issues, but grompp reports a fatal error (see subject). The particular type it complains about

[gmx-users] KALP15 in DPPC: lipid packing: deleting and shrinking lipids: why are the number of lipids not decreasing?

Dear gmx-users, I am not confident doing the lipid packing in this tutorial (using Maximin 3 instead of KALP15): http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html And my biggest problem is this error (see my hypothesized solution at the end

Re: [gmx-users] File input/output error: algorithm_parameters.mdp

On 4/1/15 4:12 PM, Poncho Arvayo Zatarain wrote: Hello, i´m working in a tutorial to generate a tpr file and i´m using grompp, my mdp file, .pdb and .top file, -o and .tpr file. I´m using this command for grompp: grompp -f dppc128.mdp -c dppc.pdb -p topol_dppc.top -o dppc128_1.tpr And it

Re: [gmx-users] Setting custom atoms in FF

On 4/1/15 4:24 PM, Alex wrote: That is the issue. I AM using -noparam, and x2top is reverting to an incorrect bond type. Which then sets off errors in grompp, because indeed it looks up the bond in ffbonded and sees nothing for the bond type just produced by x2top. As soon as I manually modify

Re: [gmx-users] simulate a multimer with one component has covalently attached prosthetic group

On 4/1/15 1:49 PM, Debajyoti Dutta wrote: Hi all, I am trying to simulate a dimer (say A2) where another protein is docked (say B) which is covalently attached with a prosthetic group. My question is how to do that. so far what i did ... I generate a gro and itp file from PRODRG

Re: [gmx-users] Setting custom atoms in FF

I am not mixing forcefield types, but I am indeed mixing angle types. I suppose I will adjust my constants so the local derivatives near equilibrium roughly correspond to what I need while sticking to the rtp default, I can't see another way around. I have tremendous respect for you guys, but I

Re: [gmx-users] Setting custom atoms in FF

On 4/1/15 4:37 PM, Alex wrote: I am not mixing forcefield types, but I am indeed mixing angle types. I suppose I will adjust my constants so the local derivatives near equilibrium roughly correspond to what I need while sticking to the rtp default, I can't see another way around. I have

Re: [gmx-users] Setting custom atoms in FF

I will certainly consider it. In all honesty, however, the situation is due to the fact that I have graphene constants that have been calculated a certain way from the Brenner potential. The problem at hand can be solved without modifying GMX code by merely calculating proper constants for _all_

Re: [gmx-users] grompp: unknown bond_atomtype

On 4/1/15 4:27 PM, Alex wrote: I think I solved it already, thanks. Entirely due to horrible mess created by the necessity to create custom atom types. I wish you guys could make the bond length tolerance an input to x2top, I really do. :) Well, I already showed you the function to modify

Re: [gmx-users] ATB

On 4/1/15 8:30 AM, Vasiliy Znamenskiy wrote: Dear All Does the type of chemical bond (single, double, triple), built by JSME Molecular Editor, directly influence on the final results of Automated Topology Builder (http://compbio.biosci.uq.edu.au/atb/ ), not by number of built protons? I built

Re: [gmx-users] grompp: unknown bond_atomtype

True, true. :) On Wed, Apr 1, 2015 at 2:29 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/1/15 4:27 PM, Alex wrote: I think I solved it already, thanks. Entirely due to horrible mess created by the necessity to create custom atom types. I wish you guys could make the bond length tolerance

[gmx-users] File input/output error: algorithm_parameters.mdp

Hello, i´m working in a tutorial to generate a tpr file and i´m using grompp, my mdp file, .pdb and .top file, -o and .tpr file. I´m using this command for grompp: grompp -f dppc128.mdp -c dppc.pdb -p topol_dppc.top -o dppc128_1.tpr And it appears two errors: File input/output error:

Re: [gmx-users] grompp: unknown bond_atomtype

On 4/1/15 2:03 PM, Alex wrote: I am working with a local copy of oplsaa.ff where I have defined a set of custom atom types in atomname2type.n2t and added the bond and angle parameters into ffbonded. x2top creates the topology without issues, but grompp reports a fatal error (see subject). The

Re: [gmx-users] grompp: unknown bond_atomtype

I think I solved it already, thanks. Entirely due to horrible mess created by the necessity to create custom atom types. I wish you guys could make the bond length tolerance an input to x2top, I really do. :) On Wed, Apr 1, 2015 at 2:18 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/1/15 2:03