[gmx-users] Periodicity in x-y plane

Hi. I have already built a lipid bilayer and I want to create a box for it and fill it with water. I used : $ gmx editconf -f renumber.gro -o newbox.gro -c -box 8 8 14 -bt triclinic and after that I used: $ gmx solvate -cp newbox.gro -cs tip4p.gro -o solvated.gro -p topol.top but when I

[gmx-users] Membrane cutt-offs

Hi! I have a question regarding to cut-off values for membranes. I know that using usual cut-offs is not appropriate for systems including membrane. Where can I find the appropriate values? -- Gromacs Users mailing list * Please search the archive at

[gmx-users] How to link connections to ligating residues?

Hello Sir,         Hopefully you are doing well. As I am new to GROMACS, I am facing problems. I read your comments and You suggested someone that "You should not need external servers to generate a heme topology; GROMOS already supports it.  It's called HEME and it's in the .rtp file. 

[gmx-users] How to connect ligating residues ??

Hello, Hope so you are doing well. Thanks a lot for your kind response. Version : 5.0.7 FF: 43a1 Spc water model. Your Suggestion: "You should not need external servers to generate a heme topology; GROMOS already supports it. It's called HEME and it's in the .rtp file. Connections to

[gmx-users] Block Copolymer

hi I want to simulate block copolymer Polyethylene- Polyethylene oxide (PE-PEO). I have the individual results of PE and PEO. My question is how to connect this two polymers and simulate? what is the procedure to make block copolymer? Thanking You -- Gromacs Users mailing list * Please search

Re: [gmx-users] GMX-PLUMED speed

Interesting finding. Have you tried leaving out the two options independently? Also would be good to try that with gromacs-2016. What is your system size and cluster usage? This sounds a phenomenal speed as well as speed up. You should probably share this on the plumed google group too. Best

Re: [gmx-users] modelling of calcium ions

The things you'll have to be most careful of include whether the calcium ion parameters you choose can get the correct coordination states (as I recall, Calcium's coordination can be quite variable experimentally, in contrast to something like magnesium, which has a more strict coordination

[gmx-users] PROTEIN LIGAND SIMULATION DYNAMICS

Hi Gromacs users, I am new to simulation dynamics. On what basis do we add water molecules to the protein ligand complex? Should we ensure that the system is fully solvated? Or, can we consider simulation without solvent (water molecules)? Thanks, Subashini.K -- Gromacs Users

Re: [gmx-users] Propylene Carbonate

Sotirios, Thanks for your response. The angle I am looking at is actually present in the molecule, but the corresponding parameters are missing from the ffbonded.itp. With the hope that white spaces won't be messed when I send this email, this is the propylene carbonate molecule with the

Re: [gmx-users] GMX-PLUMED speed

They have a forum! I do agree it is more appropriate there! Tks, X- > On 05 Feb 2017, at 17:19, Justin Lemkul wrote: > > > > On 2/5/17 3:49 AM, XAvier Periole wrote: >> >> Dears, >> >> I am using gromacs v5.1.4 with PLUMED v2.3.0. >> >> Through my experience as a novice

Re: [gmx-users] Question Regarding Hydrogen Database Error

Dr. Lemkul, I am happy to tell you that my topology has been successfully generated due to your kind assistance! Thank you so much! I will be sure to reference you when I have finished my research and am presenting it at my local science fair. Best, Elise -- Gromacs Users mailing list *

Re: [gmx-users] GMX-PLUMED speed

On 2/5/17 3:49 AM, XAvier Periole wrote: Dears, I am using gromacs v5.1.4 with PLUMED v2.3.0. Through my experience as a novice in using PLUMED, I have noticed that not writing the restraint/forces info in a file and not using a STRIDE accelerate the code significantly. Using a line such

Re: [gmx-users] Propylene Carbonate

automated builders usually produce these mistakes. I see that you already checked which atoms correspond to this error. Check first if there is an actual bond there. If it is check ffbonded if these atom types are parametrized. From:

Re: [gmx-users] modelling of calcium ions

On 2/5/17 4:18 AM, Mahboobeh Eslami wrote: Hi all GMX usersI hope you are wellI want to simulate a protein-ligand complex. There are two calcium ions in the crystallographic structure of protein. I want to keep them. I find non-bonded parameters of Ca+2. How can I use these parameter for

Re: [gmx-users] Topology error

Furthermore external servers fail to parameterize Fe, so it is of no use anyway. You should find the missing parameters in the literature. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of

Re: [gmx-users] Question Regarding Hydrogen Database Error

Dr. Lemkul, I have thoroughly inspected the contents of my PDB file and I am unsure of where the naming issue you suggested is in regard to the CH3 atom. The NMA group looks like the following: ATOM712 CA NMA A 312A 11.567 -11.364 -9.880 1.00 0.00 C ATOM713 HA1 NMA A 312A

[gmx-users] modelling of calcium ions

Hi all GMX usersI hope you are wellI want to simulate a protein-ligand complex. There are two calcium ions in the crystallographic structure of protein. I want to keep them. I find non-bonded parameters of Ca+2. How can I use these parameter for modelling of calcium ions.? Please guide

[gmx-users] GMX-PLUMED speed

Dears, I am using gromacs v5.1.4 with PLUMED v2.3.0. Through my experience as a novice in using PLUMED, I have noticed that not writing the restraint/forces info in a file and not using a STRIDE accelerate the code significantly. Using a line such as follows in the plumed parameters set: