Re: [gmx-users] Feedback wanted - mdp option for preparation vs production

So preparation turns the "warnings" into "notes"? Sounds like a good idea here. I actually do 6 runs through grompp / mdrun before my systems are ready for production. Don't think you need more flavours than that, though might need one for minimisation? Catch ya, Dr. Dallas Warren Drug

Re: [gmx-users] residue-ligand interaction energy using rerun option in mdrun

On 8/23/18 9:13 AM, vijayakumar gosu wrote: Dear Justin, Thank you for your prompt response. I have one more query that can we use the modified trajectory for rerun option to recompute interaction energies with less number of frames, since i have long trajectory as well as large complex.

[gmx-users] gmx msd and standard deviation for each dt

Dear All, I have a ring of carbons whose MSD over my simulation time I need to track. I understand that each MSD datapoint that gmx msd outputs is an average over all the carbons in the ring, but I also need the corresponding standard deviation of each average corresponding to a time step. Is

[gmx-users] Feedback wanted - mdp option for preparation vs production

Hi, In recent years, grompp has grown some more strident warnings that try to help GROMACS users understand when their .mdp choices might lead to calculations that are known not to simulate real physics. Berendsen-style weak coupling algorithms (for either temperature or pressure) are known to

[gmx-users] GROMACS 2018.3 patch release available

Hi GROMACS users, The official release of GROMACS 2018.3 is available! This release fixes several issues found since 2018.2. We encourage all users of the 2018 series to update to 2018.3. Please see the link to the release notes below for more details. You can find the code, documentation,

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 172, Issue 71

Dear Justin, Thank you for your prompt response. I have one more query that can we use the modified trajectory for rerun option to recompute interaction energies with less number of frames, since i have long trajectory as well as large complex. Vijayakumar Gosu Ph.D On Thu, Aug 23, 2018 at

Re: [gmx-users] Residue not found in topology

On 8/23/18 8:12 AM, Amir Zeb wrote: Thanks Justin, I have followed what did you suggest for .rtp entry in merged.rtp file of charmm36 ff. But i could not make .hdb file for ALY. Where can i find the H-information for ALY to insert them in merged.hdb file of charmm36 ff? Look at existing

Re: [gmx-users] Residue not found in topology

Thanks Justin, I have followed what did you suggest for .rtp entry in merged.rtp file of charmm36 ff. But i could not make .hdb file for ALY. Where can i find the H-information for ALY to insert them in merged.hdb file of charmm36 ff? Amir On Thu, Aug 23, 2018, 9:02 PM Justin Lemkul wrote: > >

Re: [gmx-users] specbonds

On 8/23/18 4:09 AM, Momin Ahmad wrote: Hi, i have two different residues and i want a bond defines between them. I know i have to use the specbond.dat file but how do i implement the additional potentials like stretching/angles/dihedrals? Is it enough to just describe them in

Re: [gmx-users] SWM4-NDP Simulation

On 8/23/18 4:38 AM, Julian Müller wrote: Hello, i'd like to simulate pure water and sodium chloride solutions using the drude polarizable SWM4-NDP model. I am new to Gromacs and don't know how to setup the calculation. I simulated SWM4-NDP boxes in LAMMPS before, but LAMMPS lacks the

Re: [gmx-users] residue-ligand interaction energy using rerun option in mdrun

On 8/23/18 6:34 AM, vijayakumar gosu wrote: Dear gromacs users, I want to calculate the interaction energies of one particular residue with RNA using rerun option. however i indexed the residue with RNA. in my mdp file i have given energy groups as a r_100 RNA. i ended up with an error Fatal

Re: [gmx-users] Residue not found in topology

On 8/23/18 7:52 AM, Bratin Kumar Das wrote: Hi You can see that only the problem is coming from hydrogen. So in pdb2gmx command use -ignh so that it ignores the hydrogen. If you use this this WARNING will not come. That's not true. The -ignh option ignores H atoms in the input

Re: [gmx-users] Residue not found in topology

On 8/23/18 6:30 PM, Amir Zeb wrote: Thanks Justin, Actually I used Parachem CGenFF server https://cgenff.umaryland.edu/ and generated the parameters for KAC. Do not generate parameters in this way. You will have a mixture of highly optimized protein parameters for all other residues,

Re: [gmx-users] Residue not found in topology

Hi You can see that only the problem is coming from hydrogen. So in pdb2gmx command use -ignh so that it ignores the hydrogen. If you use this this WARNING will not come. On Fri, Aug 24, 2018 at 4:00 AM, Amir Zeb wrote: > Thanks Justin, > > Actually I used Parachem CGenFF server

[gmx-users] residue-ligand interaction energy using rerun option in mdrun

Dear gromacs users, I want to calculate the interaction energies of one particular residue with RNA using rerun option. however i indexed the residue with RNA. in my mdp file i have given energy groups as a r_100 RNA. i ended up with an error Fatal error: "21510 atoms are not part of any of the

[gmx-users] SWM4-NDP Simulation

Hello, i'd like to simulate pure water and sodium chloride solutions using the drude polarizable SWM4-NDP model. I am new to Gromacs and don't know how to setup the calculation. I simulated SWM4-NDP boxes in LAMMPS before, but LAMMPS lacks the hardwall constraint for the charged particle on a

[gmx-users] specbonds

Hi, i have two different residues and i want a bond defines between them. I know i have to use the specbond.dat file but how do i implement the additional potentials like stretching/angles/dihedrals? Is it enough to just describe them in ffbonded.itp? Example: i have CH3 and NH as different

Re: [gmx-users] Residue not found in topology

Thanks Justin, Actually I used Parachem CGenFF server https://cgenff.umaryland.edu/ and generated the parameters for KAC. The merged.rtp file was modified by adding the KAC parameters That issue fixed, but now I'm getting the following warning which ultimately results in fatal error. WARNING: