AW: [gmx-users] Vizualization with VMD: no image appears

Hi. Try to load in a .gro file of your system first. After that, use the "load data into molecule" option to load in the .xtc. -Ursprüngliche Nachricht- Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] Im Auftrag von shch406 Gesendet: Mittwoch, 21. November 201

AW: [gmx-users] Average pressure(npt equilibration) could not reach my desired value

Hi, Did you try to plot the system pressure versus the simulation time to see if you end up at ~ 300bar? I presume it will take some time to get this high pressure and that would influence (i.e. lower) the average value. Besides of that, I'm not sure how good barostats behave for such very high

AW: AW: [gmx-users] question about the minimization

If you got the same problems with the protein only (and without any restraints), I wonder if you have any non-standard residues (i.e. ligands or protein modifications) present in your system? Because a normal protein should work just fine with the parameters you gave us. -Ursprüngliche Nachr

AW: [gmx-users] question about the minimization

Hi Eva, The change in energy in every step became smaller than the machine precision can represent (as is stated in the output). In other words: your system is minimized to a very high degree. A value of 10 for the Fmax is very low for a system like yours, even with a pure protein in water syst

AW: [gmx-users] can we generate .xtc file directly from mdrun?

Hello Albert, Yes, the settings you mentioned will give you .trr and .xtc files during mdrun. But please watch out, you have a little spelling typo in your message. It is nstxtcout. Cheers, Felix -Ursprüngliche Nachricht- Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gro

AW: [gmx-users] Adding phosphate to protein

There is a G43a1 modification available with phosphorylated amino acids in the users contribution section of the Gromacs homepage. http://www.gromacs.org/Downloads/User_contributions/Force_fields It was uploaded by Graham Smith and Justin made it compatible with the Gromacs 4.5.x versions, so m

AW: [gmx-users] a residue move in extremely large scale in MD

That's hard to judge for everyone but you, because there are too many questions left. What kind of residue is it? Is it at one of the protein termini, is it on the surface or buried by other sections? Are there interactions with other parts of the system? Did you check the RMSD or RMSF-values fo

AW: [gmx-users] Structure optimization failure

Hi Lara, with the .mdp you sent you are NOT going to perform a minimization, but a NPT equilibration run (i.e. a MD simulation, as stated in the first line). So check a tutorial of your choice to get a proper .mdp for a simple energy minimization. Greetings Felix -Ursprüngliche Nachricht--

AW: [gmx-users] membrane simulation

Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] Im Auftrag von Anirban Ghosh Gesendet: Donnerstag, 3. Mai 2012 13:39 An: Discussion list for GROMACS users Betreff: Re: [gmx-users] membrane simulation On Thu, May 3, 2012 at 4:38 PM, mailto:scapr...@uniroma3.it>> wrote:

AW: [gmx-users] Gromos87

Hi Shima, It would be number 17, but as you can see on the prefix, its deprecated (in other words outdated) and should not be used anymore (unless you really have to for some reason). Why not try a more modern force field? Cheers, Felix Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun

AW: [gmx-users] Residue 'FOR' not found in residue topology database

Hi Shima, It seems like this residue is not parameterized for the force field you want to use. Maybe check http://www.gromacs.org/Documentation/File_Formats/Gromacs_Building_Blocks if you can find it under a different name. If not, have a look at http://www.gromacs.org/Documentation/How-tos/Ad

AW: [gmx-users] Shape of box

Hi Lara, Please see "editconf -h" for the available box shapes. Which of these you use is depending on your system (or a matter of taste actually). The dodecahedron is mostly used to decrease the system volume, thus it's a good choice for the simulation of a single protein in solvent (as in your

AW: [gmx-users] the mdrun "-v"

Hey Acoot, The “–v” option simply means “verbose”, so mdrun outputs a bit more information (for example a nice finish time estimation) than it would do without “-v”. I doubt that giving a little bit more output to the console will influence the run time significantly. My advice: Just try it out

AW: [gmx-users] Not able to continue with Equilibration

Hello again, Well, I once had problems with simulations crashing randomly during production runs (sometimes after tens of nanoseconds) with the LINCS warnings you described. Switching LINCS from "all-bonds" to only "h-bonds" did the trick for me, although I never exactly figured out why. Maybe

AW: [gmx-users] Not able to continue with Equilibration

Hello, The results of the energy minimization look reasonable. Nevertheless, you should (visually) check your equilibration starting structure for problems (e.g. clashes that could not be solved by EM). It would be a good idea to concentrate on the atom numbers given in the error messages. To

AW: [gmx-users] About movie in GROMACS

Hi. Take a look at the "-center" flag of trjconv. Together with "-pbc" (and maybe also "-ur") it should be possible to center your molecules of interest in the middle of the simulation cell. Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] Im Auftrag von rama david Ge

AW: [gmx-users] Information on .mdp files

Hey. Well, it's always good to check the online documentation for such things. http://www.gromacs.org/Documentation/File_Formats/.mdp_File There you should find all information you need. Including examples and all usable keywords sorted by topic/task. Good luck, Felix -Ursprüngliche Nachr

AW: [gmx-users] problem in creating forcefield.doc

Hi. You don't have to paste anything in there. Take an empty text document and write the text you like to name your force field like into the first line. For example this GROMOS 53A6 forcefield , extended to include Berger force field parameter. Save it as forcefield.doc. That's all. Good luck

AW: [gmx-users] Regarding trajectory file

Or you could use trjconv in a little script to convert the snapshots you like to .pbd. Use the -b and -e flags to choose the respective time points. Also see http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts for the use trjconv non-interactively. Good luck. Von: gmx-u

Re:[gmx-users]-Snapshots

Hi. You will need a visualization program like VMD to get a 3D representation of your system. After reading in the .gro file, you can edit representation details and take pictures. Greetings, Felix Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] Im Auftrag

AW: [gmx-users] Bond force constant for GROMOS

08:48, Rausch, Felix escribió: Dear Gromacs-users, I would like to add a new bond type to the ffbonded.itp of the Gromos53a6 force field. For that, I tried to obtain the force constant for my new bond by performing vibrational frequency calculations with Gaussian. With th

[gmx-users] Bond force constant for GROMOS

Dear Gromacs-users, I would like to add a new bond type to the ffbonded.itp of the Gromos53a6 force field. For that, I tried to obtain the force constant for my new bond by performing vibrational frequency calculations with Gaussian. With that, I obtained the force constant in mDyne/A. My prob

Re: [gmx-users] where can I download POPC membrane file?

erent from gromacs CHARMM36 topol library. At 2011-05-30,"Rausch, Felix" wrote: Check this link given by another (unknown) mailing list user yesterday (Topic name: about POPC in Gromacs )! http://terpconnect.umd.edu/~jbklauda/research/downl

AW: Re: [gmx-users] where can I download POPC membrane file?

Check this link given by another (unknown) mailing list user yesterday (Topic name: about POPC in Gromacs )! http://terpconnect.umd.edu/~jbklauda/research/download.html Von: gmx-users-boun...@gromacs.org im Auftrag von albert Gesendet: So 29.05.2011 21:23 An: D

[gmx-users] MG-ATP

Hi. Looking at the list of building blocks available in GROMACS (http://www.gromacs.org/Documentation/File_Formats/Gromacs_Building_Blocks?highlight=building+blocks) you can find ATP as well as MG. So having a ATP-MG-complex in your simulation shouldn't be a problem. Regards, Felix

[gmx-users] Fw: trjconv -pbc and broken reside

You could try trjconv -f -s -pbc res -ur compact -center -o Good luck. Von: gmx-users-boun...@gromacs.org im Auftrag von ana johari Gesendet: Mi 27.04.2011 08:55 An: gmx-users@gromacs.org Betreff: [gmx-users] Fw: trjconv -pbc and broken reside dear justin, H

Re: [gmx-users] Atomtype CCL4 not found

I suppose the term "CCL4" is contained somewhere in the files you use (.top or #included .itp). So dont search in the force field folder but in your working directory. If you found the occurence, replace it with CCl4. For further help it would be better to know the exact error message and/or info

AW: [gmx-users] lipopeptide problem

If you want the lipid connected to the amino acid, i think it would be a good idea to add a new residue type to aminoacids.rtp which contains both, your lipid and the amino acid its connected to. You can start from the rtp entry of the amino acid and add the lipid parameters. After doing that, y

AW: [gmx-users] modified atomtypes.atp and grompp

very much for your help. Felix Von: gmx-users-boun...@gromacs.org im Auftrag von Justin A. Lemkul Gesendet: Fr 11.03.2011 13:07 An: Discussion list for GROMACS users Betreff: Re: [gmx-users] modified atomtypes.atp and grompp Rausch, Felix wrote: > >

[gmx-users] modified atomtypes.atp and grompp

Dear Gromacs users, I would like so simulate a protein with phosphorylated amino acids with Gromacs 4.5.3. To do so, I got the "ffG43a1p" forcefield available from the user contributions section (subsection force fields) and adapted the parameters given there to Gromos53a6. The problem now