Re: [gmx-users] Query regarding do_dssp program

I tried all the options.. I load gro file instead of xtc. At zero frame I gave representations new cartoon + secondary structure.. then I calculate sec str details by going on vmd timeline. I don't know what I am missing.. I am doing the same which I used all the time. Because these are two totally

Re: [gmx-users] Calculating C-alpha RMSD for coarse grained simulation

Dear Rebeta Did you visualise your trajectory? If not then kindly first do that. If the protein in your CG simulation is fluctuating a lot then the rmsd of 3.5 can make sense. Also, prepare a separate index for protein BB(backbone) bead only and use it in rmsd fitting as well as rmsd calculation.

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

On 1/13/20 9:22 AM, Qing Lv wrote: 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 a

Re: [gmx-users] Query regarding do_dssp program

On 1/13/20 9:15 AM, Sundari wrote: 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 ex

[gmx-users] A list of missing interactions

Dear Gromacs users I am facing this error during free energy calculation of protein-ligand for which I have applied restrained to some atoms of protein residue and ligand. A list of missing interactions: Restraint Pot. of 1 missing 1 Molecule type 'Protein' the first 10 missing int

[gmx-users] Calculating C-alpha RMSD for coarse grained simulation

Hi, I am new user of GROMACS. I have run coarse-grained umbrella sampling simulation in GROMACS. I had prepared the system in CHARMM-GUI. After running the simulation, now I want to calculate the RMSD of the protein. I have used the following command to remove pbc effect first- gmx trjconv -s 0A.g

Re: [gmx-users] Loading topology into vmd

Hi kenny, thanks for getting back to me. I use something similar to what you've suggested to deal with periodic boundary conditions. My current issue is that vmd will place a bond between two atoms that are close together in the first frame of the visualization even if those atoms aren't linked in

[gmx-users] cut-off scheme

Dear all, I have found in some old literatures where force field parmetrizations were done, they have used group cut-off scheme which was default in gromacs version then. Now, if I want to use those parameters in updated gromacs version, do I have to take cutoff scheme as group ? Or can I

[gmx-users] Troubleshooting Error Message: Invalid Index Group References

Hello all, I am a brand new MD/GROMACS user, and I have been trying to learn how to use GROMACS for coarse-grained simulations using the MARTINI forcefield. I was going through a tutorial on coarse-graining from the MARTINI website (http://cgmartini.nl/index.php/tutorials-general-introduction-g

Re: [gmx-users] Loading topology into vmd

Hi, I'm not sure what you mean by "bonds that aren't in the simulation", but from my experience, converting your .gro file with gmx trjconv using the -pbc mol and -ur compact options usually gives a clean visualisation. If necessary, you can also use the -center option to center a specific stru

[gmx-users] inter-chain disulfide bridges

Hello everyone, I have a problem related with a molecule with inter- and intra-chain disulfide bridges. When I convert my pdb file into a gromacs file, all the disulfide bridges are still connected (inter- and intra-chain). However, when I perform a short optimization of the structure (in v

Re: [gmx-users] charmm gui pdb to gro

*thanks sahil * *but i am interested in lipid molecule conversion not protein. I think pdb2gmx will work for protein molecules only.* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http:

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

I didn't get you. So your problem is solved using trr file or not? - Message from Lalehan Ozalp -     Date: Tue, 14 Jan 2020 12:53:54 +0300     From: Lalehan Ozalp Reply-To: gmx-us...@gromacs.org Subject: Re: [gmx-users] cannot load the xtc file (without PBC) to VMD       To: gmx-us

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

Thank you, but I haven't tried with a trr file and actually the last .trr file I've produced is em.trr. Thanks, On Mon, Jan 13, 2020 at 5:40 PM wrote: > Hii > Have you tried with the .trr file? Try the same procedure with .trr file. > Thanks > - Message from Lalehan Ozalp - >

Re: [gmx-users] charmm gui pdb to gro.

Hey, You could use pdb2gmx on the CHARMM-GUI ".pdb" output. The -ignh flag allows for ignoring preexisting hydrogen atoms if that's really required. Cheers, Sahil On 2020-01-14 12:23, Yogesh Sharma wrote: > Greetings, > hey, I want to convert the charmm gui generated pdb (membrane + protein