Re: [gmx-users] deltaG is positive after FEP

Hi, So far you have only completed one part of the simulation. You have to close the thermodynamic cycle in order to be able to calculate what the effect of the mutation is in your protein. Take a look at alchemistry.org for tutorials and relevant information on this topic. On 01 Sep 2017 7:20 A

[gmx-users] Symmetry corrections in FEP

Dear gmx-users, I'm analysing set of FEP simulations where a water molecule is decoupled from a protein. I’m using the orientational restraints as suggested by Boresch et al (doi 10.1021/jp0217839). In my simulations, the water molecule interconverts between two equivalent orientations at the w

Re: [gmx-users] -1.8 Equilibration pressure during MD simulation

Hi, Pressure can often fluctuate wildly, especially in relatively small systems. You probably won't be able to achieve a stable pressure of 1 atm, and that's not a problem. As long as your pressure fluctuates around 1 atm you should be fine (you can use running average in xmgrace to check for this

Re: [gmx-users] protein has broken after 100ns simulation

Hi, The mailing list removes attachments. Your best bet is uploading your snapshot to an image sharing service. Sometimes several uses of trjconv are required to fix pbc issues. > On 02 Jul 2016, at 08:16, Seera Suryanarayana wrote: > > Dear gromacs users, > > I have simulated protein for 10

Re: [gmx-users] Saving trajectory with different output time steps

Hi, You can use trjconv with the -skip flag to get your desired output. On 24 Jun 2016 9:19 a.m., "Sanket Ghawali" wrote: > Dear Gromacs user, > > I have 100ns trajectory in which the output steps are written every 5ps. I > would like to save the same trajectory of 100ns with the output steps >

[gmx-users] Relative FEP with restraints

Dear gmx-users, I have performed a relative FEP simulation involving a small mutation to my ligand. In order to prevent distortions to the protein structure I added harmonic position restraints to the protein backbone. Does anyone have a reference article for the correct treatment of the restrain

Re: [gmx-users] Suggested settings for using Amber force field in Gromacs

Hi, Your first stop should be the article describing the parametrisation of the force field. It might also be useful to look for articles that are doing something similar to what you want to do. > On 05 May 2016, at 14:49, Casalini Tommaso > wrote: > > Dear Gromacs users and developers, > I

Re: [gmx-users] very strange phenomenon for my production MD by gromacs

Hi, Sounds like you're experiencing periodic boundary artifacts. Take a look at the following link: http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions Dries On 13 Apr 2016 4:31 p.m., "Brett" wrote: > Dear All, > > > After energy minimization and equilibrations, I am no

Re: [gmx-users] Script for measurung and exporting distances between residues in VMD or Pymol from a gromacs simulation

Hi, You can do this using built-in gromacs tools. You want to make a suitable index group using gmx make_ndx, after which you can use gmx distance to measure the distance between your groups. Dries On 13 Apr 2016 3:50 p.m., "Faulkner, Matthew" wrote: > Hi all, > > Does anybody have a script, or

Re: [gmx-users] Preparing dual topology for free energy calculation

Hi, You should contact the tool's authors for that issue. I don't have any experience with it. Good luck Dries Hi Rompaey, Thanks for your valuable advice. As per your advice I went through the paper ( https://www.google.be/url?sa=t&source=web&rct=j&url=http://www.ncbi.nlm.nih.gov/pmc/articles/P

Re: [gmx-users] on md of protein-ligand complex

Hi, Take a look at acpype or FESetup. Those are automated tools that will do the conversion to gromacs compatible files. Dear All, For a MD of a protein-ligand complex, I intend to use AMBER99SB-ILDN protein force field for the protein part. If I use the antechamber (for GAFF force field) to pro

Re: [gmx-users] Preparing dual topology for free energy calculation

Hi, I'd recommend alchemistry.org as a good place to start. Justin's tutorial (the one you linked to) is an example of an equilibrium free energy method, not a slow growth method. As a general rule, equilibrium methods are easier to use and are recommended for people without extensive experience.

Re: [gmx-users] save the trajectory

Hi, You could use gmx mindist with suitable index groups to find out the distance between the surface and the polymer as a function of the time. Then you can use trjconv with the b and e flags to get that part of the trajectory. Kind regards Dries On 4 Mar 2016 4:11 p.m., "leila salimi" wrote:

[gmx-users] Different results for same protein's simulation in 4.6.5 and 5.0.4

On 29 February 2016 at 08:48, SAPNA BORAH wrote: > hi > Thanks for the suggestion. I will give this a shot, and remove these > restraints. > > I am unclear about what should I be looking in the log file as you > mentioned. The conformations are not just close, they are the same as the > initial c

Re: [gmx-users] Different results for same protein's simulation in 4.6.5 and 5.0.4

Hi, Looks like you might be applying positional restraints (define =-DPOSRES in your mdp file). This is standard practice for equilibration, but I don't think you want to be doing this for your production run, as this will restrain your protein to conformations rather close to your starting conform

Re: [gmx-users] Protein-ligand system simulations with GROMACS

t; > Another strange thing that it happens to my previous simulations is that, > when I ran a trial of 20 ns, the protein moves a lot (in a cubic box with > 1.0 nm of cutoff), and, at the final, it goes partially outside the box. I > know that it has to move a little, but all of this mo

Re: [gmx-users] Protein-ligand system simulations with GROMACS

Hi, These questions are quite specific to your problem. There's no way we can predict what equilibration time will suffice for your system. Your simulation time also depends on what the aim of your simulations is and what you hope to observe. That said, current simulations are generally a couple o

[gmx-users] Effect of compilers loaded at runtime

Hi, I'm wondering if the version of the intel toolchain loaded when calling mdrun affects results? My gromacs version was compiled with intel/2015b - would it matter if module intel/2016b was loaded at runtime? Thanks Dries -- Gromacs Users mailing list * Please search the archive at http://w

Re: [gmx-users] cutoff-scheme=Verlet

Hi, You might want to read this: http://www.gromacs.org/Documentation/Cut-off_schemes Basically, in the past Gromacs kept track of interactions through the group scheme (which made use of charge groups). The more recent verlet scheme doesn't use charge groups - that's what that line is telling yo

Re: [gmx-users] pdb2gmx with GROMOS

rmini, so the correct parameters should always be written. > > -Justin > > > On 2/19/16 8:14 AM, Dries Van Rompaey wrote: > >> Sure. I pasted my original mail at the bottom. >> I also followed your suggestion of trying the gromacs-master ff files, >> with >> ide

Re: [gmx-users] pdb2gmx with GROMOS

's a problem with *input* please > provide those files, the exact command and selections, etc. > > I recall there was some terminus issue, but I've replied to a few hundred > posts since then... > > -Justin > > On 2/19/16 3:50 AM, Dries Van Rompaey wrote: > &g

Re: [gmx-users] correct rlist and Verlet scheme

Hi, You have to take into account that your box-solute distance is applied on both sides of your solute. This means that your minimum periodic distance will be 2*box-solute distance. Regards Dries On 19 Feb 2016 1:21 p.m., "Timofey Tyugashev" wrote: > And here my hope for quick and easy solut

[gmx-users] pdb2gmx with GROMOS

this is a cosmetic issue or if something else is going on. My files can be found here: https://www.dropbox.com/sh/uapy2vxcprn0uje/AAA1TLME4czf8recVgV7U3koa?dl=0 Thanks Dries On 1/20/16 3:48 AM, Dries Van Rompaey wrote: >* Hi Justin and Marco, *>>* Thanks for your reply. I get this behaviour

Re: [gmx-users] Fwd: FW: PME settings in free energy calculations

Hi Mark, Thanks for your pointers. The energies obtained with a shifted potential match up a lot better. Kind regards Dries On 9 February 2016 at 14:30, Mark Abraham wrote: > Hi, > > On Tue, Feb 9, 2016 at 1:30 PM Dries Van Rompaey < > dries.vanromp...@gmail.com>

Re: [gmx-users] Fwd: FW: PME settings in free energy calculations

uploaded my log files here: > > > https://www.dropbox.com/sh/tcmqhn5fszeis27/AABcYOI6_FrjG7qoYJycf_35a?dl=0 > > > > Thanks for your time, > > Kind regards > > > > Dries > > > > On 9 February 2016 at 09:20, Mark Abraham > > wrote: > > &

Re: [gmx-users] Fwd: FW: PME settings in free energy calculations

wrote: > Hi, > > On Fri, Feb 5, 2016 at 1:32 PM Dries Van Rompaey < > dries.vanromp...@gmail.com> > wrote: > > > Hi, > > > > The corresponding mdp output section is: > > > > ; OPTIONS FOR ELECTROSTATICS AND VDW > > ; Method for doing e

Re: [gmx-users] Fwd: FW: PME settings in free energy calculations

like? > > > > Have you tried using the cutoffs above with group cutoffs, and seen > > what the difference is? > > > > On Thu, Feb 4, 2016 at 4:59 AM, Dries Van Rompaey > > wrote: > >> Hi, > >> > >> I'm using PME with the

Re: [gmx-users] Fwd: FW: PME settings in free energy calculations

Hi, I'm using PME with the default Potential-Shift-Verlet modifier. If I'm interpreting the manual and comments on the mailinglist correctly, the settings for rcoulomb-switch shouldn't affect this and PME-switching shouldn't be necessary (although there seems to have been some discussion about thi

Re: [gmx-users] Laptop features for MD simulations - recommendations

Hi, Just to expand a bit on Szilárd’s excellent answer, you can find a list of benchmarks for mobile cards here: http://www.notebookcheck.net/Mobile-Graphics-Cards-Benchmark-List.844.0.html Kind regards Dries > On 03 Feb 2016, at 15:14, Szilárd Páll wrote: > > Hi, > > What exactly do you w

Re: [gmx-users] How to visualizing gro file in pymol

Hi, Your tpr file only has information on the starting configuration (because it's a file that stores everything you need to start your simulation, not a file that contains your output). Your end point .gro file can be converted into a pdb through editconf as well. However, a better approach woul

Re: [gmx-users] Laptop features for MD simulations - recommendations

Hi Yasser, Could you give us an idea of the price range you're looking at? I'd probably try to get a laptop with a decent gpu to accelerate your work as much as possible. Unfortunately, such laptops are often pricy. Kind regards Dries On 3 February 2016 at 11:17, Yasser Almeida Hernández < yass

[gmx-users] Verlet scheme and relative free binding energy

Hi gmx-users, I have a question regarding the correct treatment of cut-offs for amber99sb-ildn in relative free binding energy calculations, using the verlet scheme. Many articles seem to use a 1.2 nm cutoff for coulomb interactions and a vdw interaction switched off between 0.9 and 1 nm (for inst

[gmx-users] Logfile incorrectly (?) has dVbonded/dl terms

Hi gmx-users, I'm currently using FEP introduce a small change in my molecule. As a first step, I'm simply removing the coulomb interactions for the part that's being transformed into dummies. No other interactions are being modified. However, in my logfile I find: Bond AngleProper D

Re: [gmx-users] pdb2gmx with GROMOS

Hi Justin and Marco, Thanks for your reply. I get this behaviour when I specify the default NH3+ and COO- termini through -ter, as well as when I don't use the -ter flag. Selecting the COOH terminus type removed the warning for the C-terminus, but selecting the NH2 terminus type did't remove the w

[gmx-users] pdb2gmx with GROMOS

Dear gmx-users, I'm experiencing the following warning while running pdb2gmx (gmx pdb2gmx -f 1AKI.pdb), selecting any of the GROMOS force fields; all others work fine. I get the same error with the -ignh flag. WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped to an

[gmx-users] Constraints in BAR

Hello everyone, I've got a question about the current implementation of BAR and constraints. Is the issue discussed in the following thread still a problem in current versions of gromacs? https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-developers/2010-October/004841.html Thanks in advance

Re: [gmx-users] pdb2gmx error

ALA 4 END On 8 October 2015 at 14:15, Dries Van Rompaey wrote: > I definitely agree that it's odd that the warning only occurs with this > specific residue. I ran a diff against the freshly downloaded AMBER03 > files, but they were identical. I also tried running it agai

Re: [gmx-users] pdb2gmx error

never crashed. It always runs to completion and mentions that the topology was successfully generated. I only get a warning during the execution of pdb2gmx. Thanks for all your help, Dries On 8 October 2015 at 13:33, Justin Lemkul wrote: > > > On 10/8/15 1:54 AM, Dries Van Rompaey wrote: &

Re: [gmx-users] pdb2gmx error

ons at the moment, so this specific warning is not that important, but I can't help but wonder if this warning means something is off in the topology. On 7 October 2015 at 23:05, Justin Lemkul wrote: > > > On 10/7/15 5:03 PM, Dries Van Rompaey wrote: > >> Thanks Justin, that ma

Re: [gmx-users] pdb2gmx error

Thanks Justin, that makes sense! I'm wondering why none of the other proline residues triggered that warning though? The same procedure works like a charm with other proteins. On 7 Oct 2015 10:59 pm, "Justin Lemkul" wrote: > > > On 10/7/15 3:01 PM, Dries Van Rom

Re: [gmx-users] pdb2gmx error

Abraham wrote: > Hi, > > Is it terminal? Are there specbonds in play? What's the GROMACS version? > What's your pdb2gmx command line? :-) > > Mark > > On Wed, Oct 7, 2015 at 8:43 PM Dries Van Rompaey < > dries.vanromp...@gmail.com> > wrote: > > >

[gmx-users] pdb2gmx error

Hi everyone, I'm getting the following warning when I try to run pdb2gmx on my protein structure: WARNING: WARNING: Residue 168 named PRO of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of type dihedral in that entry is not fo

Re: [gmx-users] Grompp checkpoint bug?

Dear Mark, Thanks for the reply. I filed a redmine bug report at http://redmine.gromacs.org/issues/1775. Let me know if there’s any other data you guys need to get this issue fixed. Kind regards Dries -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/

[gmx-users] Grompp checkpoint bug?

Hi everyone, I’m experiencing some discrepancies when I pass the checkpoint file to grompp using the -t checkpoint flag: grompp -f md.mdp -o md.tpr -p topol.top -c md_res_1.gro -t md_res_1.cpt This command results in a tpr file without any variables for barostat and thermostat: box (3x3): box

Re: [gmx-users] Number of hardware threads does not match OpenMP

Dear Szilárd, Thanks for your reply. I'll try your proposed fix. I was also wondering if the simulations performed could be affected in terms of reliability and accuracy or not (ie. do I need to redo the simulations already performed with the corrected settings)? Thanks! Dries -- Gromacs Users

[gmx-users] Effect of hardware threads mismatch on simulation

Dear gmx-users, When running a simulation of a protein in solution on my university’s cluster I get the two following notifications: Number of hardware threads detected (20) does not match the number reported by OpenMP (1). Consider setting the launch configuration manually! Non-default thread a