[gmx-users] symmetrical LJ binary mixture simulation

Hello, gromacs users. I wonder if it is possible to simulate a symmetrical LJ binary mixture implementing LJ-PME methods. The mixture is composed of A and B-type LJ particles and their sizes (sigma) are unity (=1). The interaction energy (epsilon) of A-A and B-B is unity, but heterogeneous

Re: [gmx-users] Perturbation Thermodynamic Integration

On Tue, 16 May 2017 15:13:10 -0400 Dan Gil wrote: > If you do this via decoupling ("absolute" transformation) you do that > > once for molecule A and once for molecule B. > > > I believe you are referring to the BAR method? I am trying to see if > I get the same

Re: [gmx-users] Perturbation Thermodynamic Integration

> > What does grompp from 2016.3 report? > ERROR 1 [file topol.top, line 10]: Atom 1 in molecule type 'HEPT' has different A and B state charges and/or atom types set in the topology file as well as through the mdp option 'couple-moltype'. You can not use both these methods simultaneously.

Re: [gmx-users] Protein-Ligand

On 5/16/17 1:31 PM, RAHUL SURESH wrote: Dear Justin Thank you much. About the term "curved", even am not exactly clear about it. Book by prof Pamela states that sentence. As I feel she must be explaining about much deformed protein. Well, that's too many unknowns. If you're worried about

Re: [gmx-users] Problems with large molecule simulation

On 5/16/17 1:32 PM, Tam, Benjamin wrote: Hi Justin, Thank you for replying, the problem is this: Fatal error: Atomtype Zr110418 not found For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors because the number and

Re: [gmx-users] Problems with large molecule simulation

Hi Justin, Thank you for replying, the problem is this: Fatal error: Atomtype Zr110418 not found For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors because the number and the name combine together i.e. supposed to

Re: [gmx-users] Protein-Ligand

Dear Justin Thank you much. About the term "curved", even am not exactly clear about it. Book by prof Pamela states that sentence. As I feel she must be explaining about much deformed protein. On Tue, 16 May 2017 at 7:41 PM, Justin Lemkul wrote: > > > On 5/15/17 9:12 AM,

Re: [gmx-users] Problems with large molecule simulation

Dear gromacs user, I am trying to simulate a large system, but I ran into some fundamental problems. For example in the .gro file, the name of the atoms merge with the number count: 2MOL C2 9998 3.987 2.259 6.276 2MOL C5 3.987 2.061 6.079 2MOL C11

Re: [gmx-users] Problems with large molecule simulation

On 5/16/17 1:27 PM, Ben Tam wrote: Dear gromacs user, I am trying to simulate a large system, but I ran into some fundamental problems. For example in the .gro file, the name of the atoms merge with the number count: 2MOL C2 9998 3.987 2.259 6.276 2MOL C5

Re: [gmx-users] Problems with large molecule simulation

Dear gromacs user, I am trying to simulate a large system, but I ran into some fundamental problems. For example in the .gro file, the name of the atoms merge with the number count: 2MOL C2 9998 3.987 2.259 6.276 2MOL C5 3.987 2.061 6.079 2MOL C11

Re: [gmx-users] Fwd: Issue with parallel simulations in vacuum

Thanks very much Mark In fact, the results that I find are pathological in the sense that the kinetic energy does not seem to be correctly distributed along the system: one of the proteins seems to be at much lower temperature than the other one (according to their conformational sampling; they

Re: [gmx-users] Perturbation Thermodynamic Integration

On Tue, 16 May 2017 10:28:08 -0400 Dan Gil wrote: > Thank you for the advice on the cut-off schemes and PME methods. > > What is the physical meaning of a non-interacting final state > > that has different masses from the initial state? > > > These free energy options

[gmx-users] Hydroxyl bonds rotating too much

Thank you Justin. The problematic OH is part of the cofactor molecule. This OH group is located in an extreme part of the cofactor so it apparently only interacts with solvent, not with the protein. I'm doing just now some tests of the cofactor solvated in order to check if the problem comes from

Re: [gmx-users] Perturbation Thermodynamic Integration

Thank you for the advice on the cut-off schemes and PME methods. What is the physical meaning of a non-interacting final state > that has different masses from the initial state? These free energy options was just from me trying to figure out why mass has any contributions at all. I am going

Re: [gmx-users] Fwd: Issue with parallel simulations in vacuum

Hi, In GROMACS 4.6.6 we added a fatal error for Andersen+constraints+domain decomposition with more than one domain, because it gave a temperature that is obviously too high. So, I presume Michael Shirts never implemented it to work / tested it with particle decomposition, either. Fortunately,

Re: [gmx-users] Perturbation Thermodynamic Integration

I have not really followed the previous email exchange but from this mdp file I wonder what you are trying to achieve. You seem to want to decouple all atoms of your HEPT molecule (couple-moltype, couple-intramol) from its environment but then you also change the masses. What is the physical

Re: [gmx-users] Perturbation Thermodynamic Integration

On Tue, May 16, 2017 at 3:54 PM Dan Gil wrote: > Hi, > > The latest version of Gromacs I have is 5.1. Using this version, grompp > produces no warnings or errors. > I know you won't get the new warning from the old code ;-) You'd need the latest grompp, as I've mentioned

Re: [gmx-users] Protein-Ligand

On 5/15/17 9:12 AM, RAHUL SURESH wrote: Dear Users I am tryjng to simulate protein ligand complex using charmm36ff for 100ns. I found the ligand moving away from the protein around 55ns. I don't think it s a pbc effect. Is there anything I have done wrong or Should I add any additional

Re: [gmx-users] 1-4 interactions in CHARMM force field

On 5/15/17 2:02 PM, Dawid das wrote: Dear Gromacs Users, I would like to hear your advice on scaling 1,4-interactions for both classical and QM/MM molecular dynamics simulations. I am using CHARMM27 force field. Firstly, for classical MD, according to this post

Re: [gmx-users] genion command

On 5/16/17 12:55 AM, Saumyak Mukherjee wrote: Hello Diana, You may try using the -conc flag in genion program to specify your salt concentration, along with -nname and -pname flags. The -nname and -pname options are irrelevant here. If there are fewer than 1000 waters in the system, I

Re: [gmx-users] Problem in Bootstrapping of PMF

On 5/16/17 7:15 AM, Alex wrote: Hello gromacs user, I have calculated the PMF by umbrella sampling for my system, by below command I am trying to Bootstrap my PMF, but I do not know why bsResult.xvg in whcih the error bars is stored can not be produced. The rests contain Profile, bsProfs.xvg

Re: [gmx-users] Fwd: Issue with parallel simulations in vacuum

On 5/16/17 7:26 AM, Agusti Emperador wrote: Dear GROMACS experts, I am simulating a system of two disordered proteins in vacuum. I use gromacs 4.6.5. The serial simulation works fine, but when I run it in parallel (2 processors) it gives seriously pathological results. I use particle

Re: [gmx-users] Graphene modeling

On 5/16/17 7:31 AM, ‪Mohammad Roostaie‬ ‪ wrote: In addition, I used this command "gmx x2top -f g.gro -o g.top -ff cnt_oplsaa -name CNT -noparam" and I got this error: Opening force field file ./cnt_oplsaa.ff/atomnames2types.n2t There are 6 name to type translations in file ./cnt_oplsaa.ff

Re: [gmx-users] Hydroxyl bonds rotating too much

On 5/16/17 7:03 AM, Juan José Galano Frutos wrote: Hi there: I am simulating a protein which include as a cofactor a molecule bearing some hydroxyl groups. The system is crashing from the begining of the equilibration step (after the following steps: vaccuum minimization, solvating,

Re: [gmx-users] Perturbation Thermodynamic Integration

On 5/16/17 9:53 AM, Dan Gil wrote: Hi, The latest version of Gromacs I have is 5.1. Using this version, grompp produces no warnings or errors. I am using OPLS-AA, and I didn't have any issues with it thus far. I inherited this research project though 3 years ago. Is there something you think

Re: [gmx-users] Perturbation Thermodynamic Integration

Hi, The latest version of Gromacs I have is 5.1. Using this version, grompp produces no warnings or errors. I am using OPLS-AA, and I didn't have any issues with it thus far. I inherited this research project though 3 years ago. Is there something you think I should look at with scrutiny? On

Re: [gmx-users] Perturbation Thermodynamic Integration

Hi, Yes that looks like it is the envelope of the new warning. What does grompp from 2016.3 report? (Aside, that looks like an ad hoc non-bonded scheme. As a reviewer, I'd reject that method immediately unless there was evidence that it worked well for a range of observables, and was consistent

Re: [gmx-users] Perturbation Thermodynamic Integration

Sorry, here is the mdp file: ;Integration Method and Parameters integrator = sd nsteps = 10 dt = 0.002 nstenergy= 1000 nstlog = 5000 ;Output Control nstxout = 0 nstvout = 0 ;Cutoff Schemes cutoff-scheme= group

[gmx-users] Hydroxyl bonds rotating too much

For more details, my system also has another cofactor with similar characteristics (FAD), I mean with hydroxyl groups but all is going fine with it so far (equilibration step). As I wrote before I did the following steps: 1- vaccuum minimization 2- solvating 3- neutralizing 4- minimization 5-

Re: [gmx-users] Graphene modeling

In addition, I used this command "gmx x2top -f g.gro -o g.top -ff cnt_oplsaa -name CNT -noparam" and I got this error: Opening force field file ./cnt_oplsaa.ff/atomnames2types.n2tThere are 6 name to type translations in file ./cnt_oplsaa.ffGenerating bonds from distances...atom 46There are 1

[gmx-users] Fwd: Issue with parallel simulations in vacuum

Dear GROMACS experts, I am simulating a system of two disordered proteins in vacuum. I use gromacs 4.6.5. The serial simulation works fine, but when I run it in parallel (2 processors) it gives seriously pathological results. I use particle decomposition and periodic boundary conditions, because

[gmx-users] Problem in Bootstrapping of PMF

Hello gromacs user, I have calculated the PMF by umbrella sampling for my system, by below command I am trying to Bootstrap my PMF, but I do not know why bsResult.xvg in whcih the error bars is stored can not be produced. The rests contain Profile, bsProfs.xvg are easily be calculated though. I

[gmx-users] Hydroxyl bonds rotating too much

Hi there: I am simulating a protein which include as a cofactor a molecule bearing some hydroxyl groups. The system is crashing from the begining of the equilibration step (after the following steps: vaccuum minimization, solvating, neutralizing, minimization, heating) due to -in all the

Re: [gmx-users] Unreasonably high pressure values

Dear Mark, I'm sorry for being unclear. I have rectangular box (20x5x7 nm, XYZ) where a flow should be replicated. at Z=0 and Z=7 there are two surfaces composed of gold atoms. In between there is a fluid. The system is open or periodic in the X and Y directions, but limited in the Z direction by

Re: [gmx-users] Graphene modeling

Thank you Justin, Actually, I want to simulate a small box of water with graphene and protein. You mean that I should just build and put the .n2t file in the directory where I want to run the system, and no other files are required or should not be changed.  I used the files specified in this

Re: [gmx-users] NMA eigenvectors doubts

During the calculation of the hessian matrix (the mdrun step) gromacs gives me the output: " There are: 127659 Atoms Non-cutoff electrostatics used, forcing full Hessian format. Allocating Hessian memory... starting normal mode calculation 'Protein in water' 15904 steps. Maximum force:

Re: [gmx-users] Unreasonably high pressure values

Hi, I don't understand the system very well from your description. You have two surfaces, a fluid between them, presumably periodic in the dimensions of the surface. But what do you have in the direction normal to the surface? Whatever it is, why should your parameterization of your gold atoms LJ

Re: [gmx-users] Unreasonably high pressure values

Dear Mark, Thanks for your answer. I did some experiments and I think I've located the problem. Within my simulation there are two main components: Two surfaces and a polymer fluid. These two surfaces are created by placing gold atoms in a FCC lattice (lattice parameters derived from the LJ

Re: [gmx-users] NMA eigenvectors doubts

Thanks Mark.. I am going to check all the input from the normal mode calculation. Luca Da: gromacs.org_gmx-users-boun...@maillist.sys.kth.se per conto di Mark Abraham Inviato:

Re: [gmx-users] NMA eigenvectors doubts

Hi, I suggest you go back through your workflow, paying attention to any time you selected a group of atoms for output or analysis, and reading carefully through the outputs of the various tools. If the output isn't what you expect... reconsider the input. :-) Mark On Tue, May 16, 2017 at 9:05

Re: [gmx-users] NMA eigenvectors doubts

The protein atoms are 6908. I have a membrane with 35884 atoms and water 84696. So far I calculated only the first eigenvector but as I said I can't understand why the number of row of this vector is 7952 or so. Luca Da:

Re: [gmx-users] NMA eigenvectors doubts

How many protein atoms do you have? How many eigenvectors? The program is not going to calculate the normal modes of the water molecules. Peter Sent from my iPhone > On May 16, 2017, at 8:53 AM, luca maggi wrote: > > Hi Peter, > > Thanks for your answer...but my