Re: [gmx-users] QM/MM-ORCA Point Charge Correction Error (Zoe Chan)

Hi, Does it run with the cutoff-scheme=group? Gerrit After trying a few different settings of .mdp, I found that "cutoff-scheme = Verlet" and "QMMMscheme = ONIOM" were causing the error. Would you have any idea how were these two settings linked to the generation of ".pc" file, and

[gmx-users] Distances calculation in umbrella sampling

Hello gmx users, I want to calculate binding free energy for protein-ligand complex by Umbrella sampling in Gromacs. I have extracted each frame's gro file for 500 frames after pulling simulation. Now, I want to calculate the distances between the representative gro files by executing the script

Re: [gmx-users] water molecule cannot be settled

Ok, thank you Justin. Ming On Nov 29, 2017 6:55 PM, "Justin Lemkul" wrote: > > > On 11/29/17 6:53 PM, MD wrote: > >> Hi Justin, >> Can you tell me where you spotted the broken topology? And where should I >> get in to get it fixed? >> > > "System has non-zero total charge:

Re: [gmx-users] water molecule cannot be settled

On 11/29/17 6:53 PM, MD wrote: Hi Justin, Can you tell me where you spotted the broken topology? And where should I get in to get it fixed? "System has non-zero total charge: -0.859995" Can any molecule have a fraction of an electron? Whatever you've manually parametrized is incorrect.

Re: [gmx-users] water molecule cannot be settled

Hi Justin, Can you tell me where you spotted the broken topology? And where should I get in to get it fixed? Thanks, Ming On Nov 29, 2017 6:15 PM, "Justin Lemkul" wrote: > > > On 11/29/17 3:26 PM, MD wrote: > >> Hi, >> >> I was trying to minimize a solvated structure with

Re: [gmx-users] There is no domain decomposition for n nodes that is compatible with the given box and a minimum cell size of x nm

On 11/29/17 5:43 PM, MD wrote: Hi folks, I got a fatal error when running em.mdp. Do you think if it is the .mdp that is causing this issue? My command line is : gmx mdrun -v -deffnm em The Fatal error: "There is no domain decomposition for 40 ranks that is compatible with the given box

Re: [gmx-users] mdrun (nvt.mdp) wouldn't work

On 11/29/17 5:02 PM, MD wrote: Hi gromacs folks, I was trying to do a mdrun using nvt.mdp and I got following error messages. I am not quite sure what is causing the error and I am hoping to get some help here. Is it because my starting structure is not good enough? There were some broken

Re: [gmx-users] water molecule cannot be settled

On 11/29/17 3:26 PM, MD wrote: Hi, I was trying to minimize a solvated structure with following commands but I got stuck at an error message complaining about water molecule not settled when I was trying to 'gmx mdrun -v -deffnm em'. I copied the grompp and mdrun command, log file and the

Re: [gmx-users] umbrella sampling

On 11/29/17 2:45 PM, rose rahmani wrote: Hello; would you please send me Mr.lemkul's article link ? i can't find them. It's linked here: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/01_pdb2gmx.html If you need something regarding my published research,

Re: [gmx-users] gmx distance,umbrella sampling

On 11/29/17 11:02 AM, rose rahmani wrote: Hello; would you please tell me how gmx distance calculate and write COM distance from .gro and .tpr files excactly? No one can give you an "exact" command because selections will depend on what you want to do, but in general, the syntax is here:

[gmx-users] There is no domain decomposition for n nodes that is compatible with the given box and a minimum cell size of x nm

Hi folks, I got a fatal error when running em.mdp. Do you think if it is the .mdp that is causing this issue? My command line is : gmx mdrun -v -deffnm em The Fatal error: "There is no domain decomposition for 40 ranks that is compatible with the given box and a minimum cell size of 2.42098

[gmx-users] mdrun (nvt.mdp) wouldn't work

Hi gromacs folks, I was trying to do a mdrun using nvt.mdp and I got following error messages. I am not quite sure what is causing the error and I am hoping to get some help here. Is it because my starting structure is not good enough? There were some broken residues but I had them fixed and the

[gmx-users] water molecule cannot be settled

Hi, I was trying to minimize a solvated structure with following commands but I got stuck at an error message complaining about water molecule not settled when I was trying to 'gmx mdrun -v -deffnm em'. I copied the grompp and mdrun command, log file and the error message after the command. Any

Re: [gmx-users] question of perturbing order in single topology FEP, gromacs

Hi, Asaf, Thank you very much for your suggestions, I am not sure I understand it correctly. 2017-11-29 13:22 GMT-05:00 : > Dear Peng, > > You can transform each of the molecules seperately. You can remove the nonbonded interactions of the atoms that are different >

[gmx-users] umbrella sampling

Hello; would you please send me Mr.lemkul's article link ? i can't find them. Thank you -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists *

Re: [gmx-users] question of perturbing order in single topology FEP, gromacs

Dear Peng, You can transform each of the molecules seperately. You can remove the nonbonded interactions of the atoms that are different between the compared molecules. Then, if you have only one dihedral relating the different atoms to the common atoms in each molecule it does not need to

[gmx-users] question of perturbing order in single topology FEP, gromacs

HI, all, I am recently doing some test FEP calculations to get familiar, I am preparing a system of ethane -> methanol using Amber gaff force field and single topology method. " 4 [ atomtypes ] 5 ;name bond_type mass charge ptype sigma epsilon Amb 6 c3 c3

Re: [gmx-users] Changing tau_p for parrinello-rahman made my simulation stable

Hi If I faced any issues, then I would use Berendsen NPT until the volume stabliized, rather than making arbitrary choices of lengths of time for phases. One is trying to equilibrate, so looking at the longest-timescale relevant observables makes some sense. Mark On Wed, Nov 29, 2017 at 6:05 PM

Re: [gmx-users] Changing tau_p for parrinello-rahman made my simulation stable

Hi Mark, thank you for your reply. So you would not recommend using tau_p=2.0? I did EM, Annealing (1ns), NVT (1ns), NPT (1ns), and then the simulation crashes after 15 ns. So would you recommend like 10 ns with Berendsen after NPT? Crashing after 15ns could still due to not being in

Re: [gmx-users] Can I attach two (or more) (Langevin) thermostats to one atom (or tc-group)?

Hi, No there's no support for this. I would strongly suggest using a more recent version of GROMACS, so that you get to benefit from the 6+ years of fixed bugs also ;-) Mark On Wed, Nov 29, 2017 at 5:20 PM Lovuit CHEN wrote: > Dear all, > > I am doing MD simulation for

Re: [gmx-users] Changing tau_p for parrinello-rahman made my simulation stable

Hi, P-R is well known to be unsuitable for systems that are not yet close to equilibrium, and documented accordingly. http://www.gromacs.org/Documentation/Terminology/Blowing_Up also suggests this might be an idea to avoid. Recent versions of grompp even warn if you use that together with

[gmx-users] Changing tau_p for parrinello-rahman made my simulation stable

Dear all, I had a hard time making my simulation stable. Perhaps someone has an explanation, perhaps it (just) saves someone a lot of time. However, I want to share my experience: I have a dense simulation box (80% water, 20% protein). Free simulation, no restrains, constrains on the

[gmx-users] Can I attach two (or more) (Langevin) thermostats to one atom (or tc-group)?

Dear all, I am doing MD simulation for comparatively smaller systems with Gromacs (older version of 4.5.5). I know you are allowed to attach one thermostat to each temperature coupling group you've assigned, with a particular "ref-t" and "tau-t" valuable. But I am testing the bath models, so

[gmx-users] gmx distance,umbrella sampling

Hello; would you please tell me how gmx distance calculate and write COM distance from .gro and .tpr files excactly? Best regards -Rose -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

Re: [gmx-users] Average data files with gmx analyze

Dear Justin: thank you very much! best regards! Mario Campo > > > On 11/29/17 4:35 AM, ma...@exactas.unlpam.edu.ar wrote: >> Dear GROMACS developers: >> The gmx tutorial tells me that in order to average data from columns of >> several similar files XVG, I must use gmx analize >> "gmx analyze

Re: [gmx-users] Average data files with gmx analyze

On 11/29/17 4:35 AM, ma...@exactas.unlpam.edu.ar wrote: Dear GROMACS developers: The gmx tutorial tells me that in order to average data from columns of several similar files XVG, I must use gmx analize "gmx analyze reads an ASCII file and analyzes data sets. ... Multiple sets can also be read

[gmx-users] Average data files with gmx analyze

Dear GROMACS developers: The gmx tutorial tells me that in order to average data from columns of several similar files XVG, I must use gmx analize "gmx analyze reads an ASCII file and analyzes data sets. ... Multiple sets can also be read when they are separated by & (option -n); in this case only

Re: [gmx-users] Acetylated histone with DNA

On 11/29/17 4:22 AM, Mehreen Jan wrote: Hello Hope all will be fine I have acetylated the lysine from Vienna PTM server using 54a8 force field. Lysine was successfully acetylated (KAC).I have simulated the acetylated protein by uisng 54a8ff downloaded from Vienna PTM and the expeiment

Re: [gmx-users] Metal-Protein interactions

Thank you Justin. It was helpful On Wed, Nov 29, 2017 at 7:33 AM, Justin Lemkul wrote: > > > On 11/28/17 1:00 PM, RAHUL SURESH wrote: > >> On Tue, 28 Nov 2017 at 7:14 PM, Justin Lemkul wrote: >> >> >>> On 11/28/17 4:54 AM, RAHUL SURESH wrote: >>> I am

[gmx-users] Acetylated histone with DNA

Hello Hope all will be fine I have acetylated the lysine from Vienna PTM server using 54a8 force field. Lysine was successfully acetylated (KAC).I have simulated the acetylated protein by uisng 54a8ff downloaded from Vienna PTM and the expeiment was successful at 1ns. Now we want to simulate