[gmx-users] Gromacs 2018.8 checksum

Dear Gromacs Developers, I'm trying to install the 2018.8 version of GROMACS through the Spack package manager (https://spack.io). They have packaged GROMACS, but I have noticed a SHA256 checksum mismatch. They have '3776923415df4bc78869d7f387c834141fdcda930b2e75be979dc59ecfa6ebec' on file, while

Re: [gmx-users] Error: Atoms in the .top are not numbered consecutively

Thank you Sir,. I found the typo in my topol.top file. So I changed the 'InflatGRO' to 'InflateGRO' and prompted the grompp module. However I have got the new error: Fatal error: number of coordinates in coordinate file (system_inflated.gro, 6538) does not match topology (topol.top,

[gmx-users] Intermolecular interactions in RDF

Dear All, I have 10 peptides in my system and I want to calculate the peptide-peptide radial distribution function. How can I calculate only the intermolecular interactions amongst the peptides (excluding the intramolecular peaks) without repeating the entire simulation? The manual has two options

[gmx-users] topology can't be generated by pdb2gmx with drude force field embedded

Hello everyone There's a problem that's been bothering me for a long time?? I've embedded the drude polarizable force field in gromacs via cloning the soure code from github. when I tried to generate topology via pdb2gmx, the terminal always prompts me for such an error: "Fatal error: Residue

[gmx-users] topology can't be generated by pdb2gmx with drude force field embedded

Hello everyone There's a problem that's been bothering me for a long time?? I've embedded the drude polarizable in gromacs via cloning the soure code from github. when I tried to generate topology via pdb2gmx, the terminal always prompts me for such an error: "Fatal error: Residue 'HOH' not

Re: [gmx-users] Regarding system shrunk

You did not mention the type of surface, but in real life an extruded polymer is under stress and you must restrain the ends. As in real life a heated uncrosslinked polymer will shrink. The system probably behaved appropriately PB > On Dec 9, 2019, at 11:31 AM, Mijiddorj B wrote: > > Dear

[gmx-users] A Gromacs Port of the amber LIPID17 force field

Hi Gmx user, I have made a gromacs port of the amber LIPID17 force field and the files are available at https://zenodo.org/record/3561004. The user can generate the lipids in amber and use it with the force field directly. Or the lipid bilayer can be generated using charms-GUI and a script

Re: [gmx-users] solvent evaporation modeling

Dear Anders and Kalil, Thank you for your answers and for sharing the scripts. I will help a lot. Best, On Tue, Dec 3, 2019 at 5:12 PM Anders Støttrup Larsen wrote: > Hi Sako > > I did something similar where I dehydrated a system of water molecules, in > my case a crystal but the principles

Re: [gmx-users] The total charge is not integer : -0.00465

Dear Mark, Thank you for your suggestion. That was true. I solved the problem. Best, On Fri, Dec 6, 2019 at 3:39 AM Mark Abraham wrote: > Hi, > > If, for example, you inserted 465 polymer molecules each with charge -.001 > then the most appropriate path forward is to make the total charge of

[gmx-users] Regarding system shrunk

Dear GMX users, I study the interaction between polymer and surface interactions. Polymer parameters were prepared by cgenff, and the parameters of the surface were solved by INTERFACEFF. I performed short simulations, however, the system was shrunk. I used the standard mdp file of charmm-gui

[gmx-users] calculation of tilt angle of helix against the bilayer normal

hi, i want to calculate the tilt angle of helix against the bilayer normal. iam using this command *gmx helixorient -s *.tpr -f *.xtc -n helix.ndx -oaxis -ocenter -orise -oradius -otwist -obending -otilt -orot* my question 1. how can i calculate the angle, so that angle can be calculated against

Re: [gmx-users] Chemical Shifts prediction using gmx chi -shift

Dear Christian, Thanks for your answer. Correct me if I'm wrong: the **-shift.dat grids contain chemical shift deviations compared to a set of reference (amino-acid-dependent) chemical shifts (taken from table 2 of "D. S. Wishart and A. M. Nip, Protein Chemical Shift Analysis: A Practical

[gmx-users] Performance GROMACS on GPU

Hi, I run three simulations on 1 node with 3 GPU by using an increasing number of GPUs. This is my system: ___ 1 node with total 36 cores, 72 logical cores, 3 compatible GPUs GROMACS version:2018.2 Precision: single

Re: [gmx-users] (no subject)

Ok i will try, thank you so much On Mon, 9 Dec 2019, 1:07 pm Tasneem Kausar, wrote: > This problem also occurs in gromacs-5.1.4. Try higher version. We have done > these calculations on gromacs-2016. > > On Mon, Dec 9, 2019 at 10:49 AM shakuntala dhurua < > madhu.dhuru...@gmail.com> > wrote: >

Re: [gmx-users] Chemical Shifts prediction using gmx chi -shift

Hello Florent, The tool is based on  "D. S. Wishart and A. M. Nip", "Protein Chemical Shift Analysis: A Practical Guide", "Biochem. Cell Biol.", 76, 1998, "153-163" It reads chemical shift reference data on a phi-psi-angle grid from ca-shift.dat, cb-shift.dat, ha-shift.dat and co-shift.dat.