[gmx-users] charmm gui pdb to gro.

Greetings, hey, I want to convert the charmm gui generated pdb (membrane + protein) to gromacs readable file. charmm generated lipids contain hydrogen atoms and naming differences. I tried doing it manually but couldnt succeed. Is there any script available for atom renaming and reordering? I als

Re: [gmx-users] Error bar for umbrella sampling?

Error bar will be directly given from gmx wham by bootstrap method. On Tue, Jan 14, 2020 at 8:13 AM Qing Lv wrote: > Thank you Alexander and Quyen. I will try these tools. > > > Qing > > > > > > At 2020-01-14 01:01:31, "Александр Лашков" wrote: > >In pymbar package error estimate directly. Exam

[gmx-users] Loading topology into vmd

Hello all, I'm just wondering how people load topologies for systems simulated in gromacs into vmd. It is very annoying to have bonds that aren't in the simulation placed in the visualisation. I'm wondering if anyone has a solution that is easier than simply creating a psf file of the .gro system

Re: [gmx-users] Error bar for umbrella sampling?

Thank you Alexander and Quyen. I will try these tools. Qing At 2020-01-14 01:01:31, "Александр Лашков" wrote: >In pymbar package error estimate directly. Example usage this package for >umbrella sampling can be found on github page for this package >Alexander > >пн, 13 янв. 2020 г., 17:35

Re: [gmx-users] Error bar for umbrella sampling?

In pymbar package error estimate directly. Example usage this package for umbrella sampling can be found on github page for this package Alexander пн, 13 янв. 2020 г., 17:35 Qing Lv : > Dear All, > > > I wonder if the error bars are necessary for umbrella sampling in PMF > calculation? If yes, h

Re: [gmx-users] Error bar for umbrella sampling?

Hi there, The statistical errors can be estimated by g_wham. Check this article: Hub, J. S., De Groot, B. L., & Van Der Spoel, D. (2010). G-whams-a free Weighted Histogram Analysis implementation including robust error and autocorrelation estimates. *Journal of Chemical Theory and Computation*, *6*

[gmx-users] Number of bins for wham and umbrella sampling / PMF

Dear Gromacs users, I want to perform umbrella sampling in order to calculate the PMF for pulling a molecule from a surface. For evaluation, I use gmx wham with bootstrapping, and Gromacs version is 2018.4. I've noticed that my results strongly depend on the number of bins, with peak heights d

Re: [gmx-users] cannot load the xtc file (without PBC) to VMD

Hii Have you tried with the .trr file? Try the same procedure with .trr file. Thanks - Message from Lalehan Ozalp -     Date: Mon, 13 Jan 2020 13:35:01 +0300     From: Lalehan Ozalp Reply-To: gmx-us...@gromacs.org Subject: [gmx-users] cannot load the xtc file (without PBC) to VMD  

[gmx-users] com motion and position restraints may cause artifacts

dear all, I installed gromacs 2020 and I now get the following message during equilibration: NOTE 1 [file nvt.mdp]: Removing center of mass motion in the presence of position restraints might cause artifacts I do not recall seeing this with gromacs 2018. In which cases are artifacts created?

[gmx-users] Error bar for umbrella sampling?

Dear All, I wonder if the error bars are necessary for umbrella sampling in PMF calculation? If yes, how should the error bars be calculated? Need I do 2~3 repeats (with different random initial velocites assigned)? Thanks, Qing -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] atom moved too far

Justin thank you. I installed gromacs 2020, just gmx, (not gmx_mpi) and the simulation is currently at ~75 ns so I think that solved the problem. It seems to me that I either did something wrong installing gmx_mpi (gromacs 2018) or I should not run gmx_mpi on a single node. gmx 2020 also gives ~

Re: [gmx-users] Is minimization and equilibration needed for umbrella sampling?

Thank you, Justin. I start each run by randomly generate velocities at 300K, and each run is quite stable. So, is it appropriate to regard the first 20 ps (this is a QM/MM MD) of each run as the equilibration and just discard this 20 ps in the final wham analysis? Best, Qing At 2020-01-13 2

Re: [gmx-users] Query regarding do_dssp program

Yes, Sir, I made the gro file for a particular time by using "gmx trjconv" command ( also checked with -pbc mol, whole, no_jump options ) but every time the 2ndary structure visualization in vmd is different from dssp sequence of residues in gromacs. Fox example in my protein dssp shows 8 residue

Re: [gmx-users] Query regarding do_dssp program

On 1/13/20 7:22 AM, Sundari wrote: Hello Dear, Actually I was thinking the same i.e. gromacs use "dssp" criteria and vmd use "stride" algorithm for secondary structure determination. But the expected error in the two algorithms should not be more than 5% according to the literature. Here, In

Re: [gmx-users] cannot load the xtc file (without PBC) to VMD

On 1/13/20 5:35 AM, Lalehan Ozalp wrote: Dear all, I have a question regarding loading .xtc file (with no periodic boundary conditions) to VMD which I generated before. To this end, I had used the command: trjconv -f md_0_10.xtc -s md_30.tpr -n index.ndx -o noPBC.xtc -pbc mol -ur compact -cent

Re: [gmx-users] Is minimization and equilibration needed for umbrella sampling?

On 1/10/20 11:02 AM, Qing Lv wrote: Dear Colleagues, I am doing a QM/MM umbrella sampling to calculate the PMF of an enzymatic reaction. The initial coordinates (with solvents and ions) for each sampling window were extracted from previous trajectories. The reaction coordinate (bond lengt

Re: [gmx-users] Query regarding do_dssp program

Hello Dear, Actually I was thinking the same i.e. gromacs use "dssp" criteria and vmd use "stride" algorithm for secondary structure determination. But the expected error in the two algorithms should not be more than 5% according to the literature. Here, In my case, the structure contains a lot of

[gmx-users] cannot load the xtc file (without PBC) to VMD

Dear all, I have a question regarding loading .xtc file (with no periodic boundary conditions) to VMD which I generated before. To this end, I had used the command: trjconv -f md_0_10.xtc -s md_30.tpr -n index.ndx -o noPBC.xtc -pbc mol -ur compact -center and selected *protein* for centering, and *

Re: [gmx-users] Cut off (1.2 -1.5 nm) with OPLS forcefield

Hi, A general criteria is to apply the short and long range interaction setting used in the parametization procedure. Each force field has its own parameterization strategy. Among other that guarantees parameters consistency and results reproducibility. Another story is if you are performing your

Re: [gmx-users] Query regarding do_dssp program

Hi, VMD and dssp may use a slightly different criteria to define a beta sheet. First I will check in literature if the criteria are the same. In some case, it occur that the the atom types (e.i H) are not properly recognized by the software, and thus secondary structure element can not be determ