Re: [gmx-users] pbc nojump with replica exchange behaves differently than with regular MD

am stuck with this two options. So my question is whether is there is a way to use the tpr for a xtc trajectory that contains fewer atoms than the ones defined in the tpr? Or another workaround? Thanks, Ramon On 11/28/19 9:44 AM, Ramon Crehuet wrote: > Dear all, > As a follow-up

Re: [gmx-users] pbc nojump with replica exchange behaves differently than with regular MD

? Could it be that in an exchange attempt only the coordinates of the atoms are exchanged between temperatures but not the box size? (the dynamics use a Parrinello-Rahman barostat). Thanks again. All the best, Ramon - On 28 Nov, 2019, at 11:49, Ramon Crehuet wrote: > Dear all, >

[gmx-users] pbc nojump with replica exchange behaves differently than with regular MD

Dear all, I have run a temperature replica exchange and I would like to analyze the resulting trajectory for a given temperature (i.e. not following a replica across temperatures using demux.pl). The simulations consist of a single protein chain. I can easily generate have a whole molecule, na

[gmx-users] How to change to heavyh in an equilibrated system

Dear all, For testing reasons, I would like to compare a system that I have setup using heavy hydrogens (-heavyh option in pdb2gmx) to exactly the same system without using heavy hydrogens. I could redo all the system setup starting from the pdb2gmx, but I would like to avoid that. That setup

[gmx-users] Error with virtual sites

Dear all, I am trying to setup the simulation of a system composed of several peptide chains in water, using Charmm27 FF in TIP3P water. All residues are standard and I've done similar protein preparations other times. This time, however, I've got the following error when calling grompp for

[gmx-users] Does gmx distance correct for broken molecules from pbc?

whole, but apparently it doesn't in my case. Is there a way to calculate the distance directly from the original trajectory? Thanks in advance, Ramon -- Ramon Crehuet Cientific Titular (Assistant Professor) Institute of Advanced Chemistry of Catalonia IQAC - CSIC schol

[gmx-users] Amber03ws includes an unexpected dihedral with atoms -C N CA CB

Dear all, I would like to use the Amber03ws force field described in Best, Zheng and Mittal, J. Chem. Theor. Comput., 10, 5113-5124, 2014. This force field is contributed in http://www.gromacs.org/Downloads/User_contributions/Force_fields When using it, Gromacs reports a warning about a CB ato

[gmx-users] B-FACTOR

The B-factor is indeed RMSF, precisely 8*pi**2*RMSF. At least formally. In practice it is the result of the refinement procedure that is used in crystallography. If you would like to calculate it, you should simulate a crystal. This is almost never done, but Bojan Zagrovich did it and compared

[gmx-users] Parameterizing Acetylated lysine: need for impropers?

Dear all, I am trying to adapt to Gromacs the parameters of acetylated lysine from 2 sources. First from http://ares.tamu.edu/FFPTM/ This webpage gives parameters in AMBER format. I've created a new residue in aminoacids.rtp coying the data from the Amber file. The Amber file contains the fo

[gmx-users] vsites with CHARMM force fields

Dear all, I am simulating a system with CHARMM36m force field. Following the recommendations in the mailing list and the gromacs web page, I constrained only h-bonds (constraints = h-bonds). In that case, does it make sense to use virtual sites to allow 4fs time step? In other words, if vs

[gmx-users] Replica exchange: exchanging pressures

Dear all, I'd like to run a replica exchange, but instead of exchanging temperatures, I would like to exchange pressures. I know this does not help enhance sampling, but I would like to create several ensembles at different pressures and I want them to mix, as RE does. After preparing and equi

[gmx-users] rotacf in Gromacs 5.1 gives unexpected results

C(t)) I compiled Gromacs 5.1 with the standard options and `make check` passed all the tests. Is this a known issue? Is it a problem with my compilation? How can I check it? Thanks in advance, Ramon -- Ramon Crehuet Cientific Titular (Assistant Professor) Institute of Advanced Chemistry of

[gmx-users] S**2 order parameter from a trajectory

*increase* to 1.0025. Is this normal? I don't think I can fit that to a model free with two parameters S**2 + (1-S**2)*exp(-t/tau) ... Thanks in advance, Ramon -- Ramon Crehuet Cientific Titular (Assistant Professor) Institute of Advanced Chemistry of Catalonia IQAC - CSIC http://www.iqac.csic.es/

Re: [gmx-users] How to determine box shape and parameters from a run

   6.63682 Thanks again, Ramon On 11/3/15 5:56 AM, Ramon Crehuet wrote: > Dear all, > This is a very simple question, but I could not find the answer in the > documentation. Some time ago I run a simulation and now I don't remember the box > shape and

[gmx-users] How to determine box shape and parameters from a run

inted somewhere or I need to calculate it from the parameters. Thanks in advance, Ramon PS. My log contains Box-X Box-Y and Box-Z parameters. Does that mean I used a rectangular box? -- Ramon Crehuet Cientific Titular (Assistant Professor) Institute of Advanced Chemistry of Catalonia IQAC - CSIC