Re: [gmx-users] pcoupl Berendsen

> A pressure without an error bar is a meaningless value. The fluctuations > of pressure in most systems are on the order of tens or hundreds of bar, > meaning your result is indistinguishable from the target value. To help illustrate this, here is one example of the type of pressure fluctuation

[gmx-users] Gromacs Neighbor List Output

Hello, I noticed that gromacs has an environment variable that seems to allow it to output neighbor lists. I haven't been able to figure out how to use it. Does anyone have an example of how this could work? Thanks, Adriaan Riet -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Bond Decomposition Error

Hello Tom, I got something like decomposition errors when running in GPU clusters, and later I found it is because of PBC unit cell angles. You can try to use trajconv to get out of one pdb file from your simulation box. If the unit cell is non-90degree, it will cause this domain decomposition

[gmx-users] Bond Decomposition Error

Hi everyone, I've recently gotten a simulation of a 2D crystal surface set up in GROMACS using a combination of x2top and periodic-molecules. Things run okay for me when I do small-scale tests on a single core (minimization, NVT equilibration, etc), however when I try to scale this up

Re: [gmx-users] pdb2gmx fatal error

Dear Justin, Thank you for your response. Yet, I have not been able to solve the problem. The structure looks fine but gromacs is complaining about a dangling atom at one of the terminal ends, if I choose no terminal to be added. While, assigning a terminal to the ends (which I don't understand

[gmx-users] 4. Re: 5. Re: 3. Re: Strange pullx coordinates (PMF

Hello Justin I still don't understand where Gromacs takes the x coordinates in the output pmf with g_wham If I run g_wham with tpr-files and pullf-files without the pullx-files -it tpr-files.dat -if pullf-files.dat I get a profile which means that g_wham does not take the X-coordinates in the

[gmx-users] Assigning charge to closely related functional group

Hi All, Following is the structure of the molecule, which I wish to parameterize. CH3 O | || CH3 - C - O - C - | CH3 It is a peptide capping reagent. The last carbon will form bond with the NH2 group of the peptide. I have generated the the

Re: [gmx-users] DispErsion correction

Dear Justin and Dallas Thank you for your replying I have another problem in minimizing and NVT run of my complex, including a protein and a peptidic ligand which the ligand has 2 phosphotyrosine residues. I generated a topology file of ligand using ff14sb in ambertools 16 and then converted the

Re: [gmx-users] start the simulation of the last stopping point.

Hello, you can find information on how to extend simulations here: http://manual.gromacs.org/documentation/current/user-guide/managing-simulations.html Cheers Paul On 2018-11-08 14:23, Edjan Silva wrote: Dear fellow scientists, I'm doing a 40ns simulation between DNA and a small molecule.

[gmx-users] start the simulation of the last stopping point.

Dear fellow scientists, I'm doing a 40ns simulation between DNA and a small molecule. It occurred that around 30 nanoseconds, the computer hung up. How do I start the simulation from the 30 nanoseconds performed? -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] pcoupl Berendsen

On 11/8/18 7:50 AM, Gonzalez Fernandez, Cristina wrote: Dear Gromacs users, In my simulations, I have specified ref_p= 1bar but after MD simulation I obtain pressures equal to 0.19 bar (even A pressure without an error bar is a meaningless value. The fluctuations of pressure in most

Re: [gmx-users] Topology include file "tip3p.itp" not found

On 11/8/18 5:20 AM, Rahma Dahmani wrote: Dear Gromacs Users, I want to run MD simulation of ligand in water box , for that i have manually constructed a topology file of my ligand with antechamber tools then i used GROMACS instructions to build a box of water molecules (ligand_solv.gro),

Re: [gmx-users] DispErsion correction

On 11/7/18 5:06 PM, Dallas Warren wrote: Paper explaining dispersion correct, and what it is: http://dx.doi.org/10.1021/jp0735987 And note that not all force fields are parametrized in such a way that they make use of dispersion correction. -Justin Catch ya, Dr. Dallas Warren Drug

Re: [gmx-users] combining multiple MD proteins,

On 11/7/18 2:46 PM, daniel madulu shadrack wrote: Dear, I want to combine proteins to merge into single pdb but I get this error below. Command line: gmx trjcat -f 10ns.pdb 15ns.pdb 40ns.pdb 60ns.pdb 90ns.pdb -o all.pdb You don't need trjcat, just use the standard Linux cat to combine

[gmx-users] pcoupl Berendsen

Dear Gromacs users, In my simulations, I have specified ref_p= 1bar but after MD simulation I obtain pressures equal to 0.19 bar (even with long simulation times) when using pcoupl=Parrinello-Rahman. I know that Parrinello-Rahman is recommend for production runs and Berendsen for NPT

[gmx-users] Topology include file "tip3p.itp" not found

Dear Gromacs Users, I want to run MD simulation of ligand in water box , for that i have manually constructed a topology file of my ligand with antechamber tools then i used GROMACS instructions to build a box of water molecules (ligand_solv.gro), when i tried to minimize my structure (with

Re: [gmx-users] Periodic saving of checkpoint file

Hi Mark, Thank you for your answer. I didn't know this option. From what I have read, eneconv is for reading parameters for Nose-Hoover or Parrinello-Rahman coupling. Thus, if I am doing first an NVT simulation with the velocity-rescale thermostat or a Langevin dynamics, I don't need the .edr