Re: [gmx-users] Compiling g_correlation

On 4/27/16 4:49 PM, Jorge Fernández de Cossío Díaz wrote: Is there a way to do the conversion? Perhaps a combo of trjconv from 4.6.5 and 3.3? I'm thinking about it but cannot figure out a combination to work. No, because there's no magic -make_compatible_with_prehistoric_version argument :)

Re: [gmx-users] Compiling g_correlation

Is there a way to do the conversion? Perhaps a combo of trjconv from 4.6.5 and 3.3? I'm thinking about it but cannot figure out a combination to work. On Wed, Apr 27, 2016 at 4:38 PM, Mark Abraham wrote: > Like Justin said, you'll need a new .tpr made by 3.3. Hopefully that is > possible. That d

Re: [gmx-users] Compiling g_correlation

Like Justin said, you'll need a new .tpr made by 3.3. Hopefully that is possible. That doesn't mean you run another simulation in 3.3 ;-) Mark On Wed, Apr 27, 2016 at 9:22 PM Jorge Fernández de Cossío Díaz < j.cossio.d...@gmail.com> wrote: > I got g_correlation compiled. Now I'm trying to use it

Re: [gmx-users] Compiling g_correlation

I got g_correlation compiled. Now I'm trying to use it on a trajectory generated with Gromacs 4.6.5. I get the following error: Reading file topol.tpr, VERSION 4.6.5 (single precision) --- Program g_correlation, VERSION 3.3.4 Source code file: t

Re: [gmx-users] Compiling g_correlation

Great! That fixed it. Just change the line "#include " in traj_stuff.h to "#include ". Thanks On Wed, Apr 27, 2016 at 2:48 PM, Jorge Fernández de Cossío Díaz < j.cossio.d...@gmail.com> wrote: > Great! That fixed it. > Just change the line "#include " in traj_stuff.h to "#include > ". > Thanks >

Re: [gmx-users] Compiling g_correlation

Great! That fixed it. Just change the line "#include " in traj_stuff.h to "#include ". Thanks On Wed, Apr 27, 2016 at 2:40 PM, Kutzner, Carsten wrote: > > > On 27 Apr 2016, at 19:42, Jorge Fernández de Cossío Díaz < > j.cossio.d...@gmail.com> wrote: > > > > I compiled gromacs 3.3.4, and pointed

Re: [gmx-users] Compiling g_correlation

> On 27 Apr 2016, at 19:42, Jorge Fernández de Cossío Díaz > wrote: > > I compiled gromacs 3.3.4, and pointed the g_correlation Makefile to its > directory, But compilation of g_correlation still complains that it can't > find "fatal.h". Any ideas? it has been renamed to gmx_fatal.h Carsten >

Re: [gmx-users] Compiling g_correlation

I compiled gromacs 3.3.4, and pointed the g_correlation Makefile to its directory, But compilation of g_correlation still complains that it can't find "fatal.h". Any ideas? On Wed, Apr 27, 2016 at 1:21 PM, Jorge Fernández de Cossío Díaz < j.cossio.d...@gmail.com> wrote: > Okay, will try to compil

Re: [gmx-users] Compiling g_correlation

On 4/27/16 1:17 PM, Jorge Fernández de Cossío Díaz wrote: Okay, will try to compile using gromacs 3.3. But my simulation was run in 4.6.5. Will I be able to use g_correlation to analyze it? You'll need a new .tpr file, at minimum. The force fields that were supported were much more limite

Re: [gmx-users] Compiling g_correlation

Okay, will try to compile using gromacs 3.3. But my simulation was run in 4.6.5. Will I be able to use g_correlation to analyze it? On Wed, Apr 27, 2016 at 11:09 AM, Sarath Chandra < sarathchandrada...@gmail.com> wrote: > You have to use gromacs 3.3 and also will need lamboot and other > depende

Re: [gmx-users] 5. LINCS warning of QMMM simulation (andrian)

On 4/27/16 11:06 AM, andrian wrote: Hi, anyone can help me ??? :( People contribute to this list when free time allows; GROMACS provides no promise of immediate technical support. Perhaps the people who can best answer your question are busy, sleeping, or only subscribe to digests that c

Re: [gmx-users] Compiling g_correlation

You have to use gromacs 3.3 and also will need lamboot and other dependencies. Let me know how you progress. I recently installed it On Apr 27, 2016 8:35 PM, "Jorge Fernández de Cossío Díaz" < j.cossio.d...@gmail.com> wrote: > I'm trying to use g_correlation ( > http://www.mpibpc.mpg.de/grubmuelle

Re: [gmx-users] 5. LINCS warning of QMMM simulation (andrian)

Hi, anyone can help me ??? :( On 27/04/16 01:48, Groenhof, Gerrit wrote: Hi, Are you able to run a stable MM simulation with that system? Can you rule out that the system is not strained somewhere? Where do the starting coordinates come from? best, Gerrit Message: 5 Date: Tue, 26 Apr 201

[gmx-users] Compiling g_correlation

I'm trying to use g_correlation ( http://www.mpibpc.mpg.de/grubmueller/g_correlation) to compute the correlations in a MD simulation. I am using GROMACS 5.1.2 and 4.6.5 (have both). When I try to compile g_correlation, I get this error: cc -O6 -fomit-frame-pointer -finline-functions -Wall -Wno-un

Re: [gmx-users] Analysis of the protein-protein binding

Thanks for the suggestions Catarina! Actually I am not sure regarding accuracy of how the h-bonds and saltbridges will be modelled during CG simulations :-) So right now I will be interesting to focus on some very general sollutions like contact maps, inter-subunit (inter-chain in case of my syste

Re: [gmx-users] Analysis of the protein-protein binding

Hi James, Trajectory analysis are highly dependent on the system of study, namely on what you want to get from your simulations. Also, the protocol you described is a fairly common one. Having said that, a good strategy is probably starting by checking the literature for ways to caracterize bindin

[gmx-users] Analysis of the protein-protein binding

Dear Gromacs Users! I am looking for some non-complicated analysis of protein-protein association simulation. Firstly using MARTINI model I have simulated association between water soluble protein and some water-exposed part of the membrane protein mediated mainly by the electrostatics attraction

Re: [gmx-users] 5. LINCS warning of QMMM simulation (andrian)

Hi Gerrit and all users, do you have an idea about this problem ? now, i attached all my simulation files... hope someone can help.. thanks in advance cheers On 27/04/16 01:48, Groenhof, Gerrit wrote: Hi, Are you able to run a stable MM simulation with that system? Can you rule out that

Re: [gmx-users] 5. LINCS warning of QMMM simulation (andrian)

Hi Gerrit and all users, do you have an idea about this problem ? now, i attached all my simulation files... hope someone can help.. thanks in advance cheers On 27/04/16 01:48, Groenhof, Gerrit wrote: Hi, Are you able to run a stable MM simulation with that system? Can you rule out that

Re: [gmx-users] Simulation getting slower and ultimately crashing

Hi, I think I forgot to provide the md.log file in the previous mail. So, here it is: "md_tric.log" 1513L, 76430C 1,1 Top av. #atoms communicated per step for force: 2 x 552.4 av. #atoms communicated per step for LINCS: 2 x 0.0 Average load imbalance:

[gmx-users] Simulation getting slower and ultimately crashing

Hi, I am simulating a nucleic acid in the presence of a 15X15 single walled carbon nanotube using CHARMM 27 force field and TIP3P water model. In my previous published work, I did the simulation inside a cubic box and everything ran fine but as of now whenever I am switching over to a triclini

Re: [gmx-users] distance restraint between 2 molecules

Hi, Or use the pull code. Kind regards, Erik > On 27 Apr 2016, at 08:09, Catarina A. Carvalheda dos Santos > wrote: > > Hi Hong, > > You have (at least) two options: > > 1) Edit the specbond.dat file so that the pdb2gmx creates a covalent bond > between the ligand and the protein (the bond

Re: [gmx-users] Protein is Jumping from water Box

Dear Abid, I wouldn’t call it an issue nor an error. Your protein is still interacting with some periodic copy of the solvent molecules. See http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions. Kind regards, Erik On 27 Apr 2016, at 05:23, Abid Channa mailto:abid_chan

Re: [gmx-users] distance restraint between 2 molecules

Hi Hong, You have (at least) two options: 1) Edit the specbond.dat file so that the pdb2gmx creates a covalent bond between the ligand and the protein (the bonded terms for this interaction have to be present in the force field files); 2) Use position restrains on these two atoms instead. Chose