Re: [gmx-users] residue error

This is nonstandard residue so GROMACS does not have database about it. you need to generate database consistent with your forcefield On Mon, Feb 26, 2018 at 11:22 PM, Radhika Arora wrote: > Hello, > > I face an error Residue 'BGL' not found in residue topology

[gmx-users] Simulation for Metalloprotein

Hi users, Whether it is possible to run the simulation for protein with metal (calcium) ? If so, what are the force fields that can be used ? How those force fields must be altered in order to run the simulation. -- Sankaran.s.v bbin -- Gromacs Users mailing list * Please search the archive

Re: [gmx-users] cpu/gpu utilization

Hi, Please provide details, e.g. the full log so we know what version, on what hardware, settings etc. you're running. -- Szilárd On Mon, Feb 26, 2018 at 8:02 PM, Mahmood Naderan wrote: > Hi, > > While the cut-off is set to Verlet and I run "gmx mdrun -nb gpu -deffnm >

[gmx-users] cpu/gpu utilization

Hi, While the cut-off is set to Verlet and I run "gmx mdrun -nb gpu -deffnm input_md", I see that 9 threads out of total logical 16 threads are running on the cpu while the gpu is utilized. The gmx also says No option -multi Using 1 MPI thread Using 16 OpenMP threads I want to know, why 9

[gmx-users] Anisotropic Pressure Coupling

Hello, I've been trying to run a simulation using anisotropic pressure coupling (I want to allow the box to adjust to the right size for a zero-pressure simulation). I am using the following settings in the .mdp file: Pcoupl = Berendsen pcoupltype = anisotropic

Re: [gmx-users] About and index file of a monolayer...

This is actually pretty challenging to do, but is possible with the right technique. Have a look at the selection commands in gmx select, which allows the specification of x,y,z positions. If you know the mid plane of one leaf in your bilayer, you can specify a molecule type and only take

[gmx-users] About and index file of a monolayer...

Hello gromacs users: If i have a bilayer with lipids A & B and i want to create an index file for the upper and lower monolayer of one lipid, for example: lipid A-UPPER and lipid B-UPPER. Also, lipid A-LOWER and lipid B-UPPER. How can i do that using -n index.file? -- Gromacs Users mailing

Re: [gmx-users] residue error

On 2/26/18 11:22 AM, Radhika Arora wrote: Hello, I face an error Residue 'BGL' not found in residue topology database. Please let me know how shall i rectify this and what do i need to write in place of BGL. HETATM 1700 C BGL 1 29.680 -48.720 -19.563 0.00 -0.02 .177 C HETATM

[gmx-users] residue error

Hello, I face an error Residue 'BGL' not found in residue topology database. Please let me know how shall i rectify this and what do i need to write in place of BGL. HETATM 1700 C BGL 1 29.680 -48.720 -19.563 0.00 -0.02 .177 C HETATM 1701 C BGL 1 13.970 -44.542 -17.378

Re: [gmx-users] walls with slab of water

Hi, I would use a flat-bottomed position restraint in Z-direction for this purpose, see the Gromacs manual. Cheers, Jochen Am 25.02.18 um 10:17 schrieb Adriano Santana Sanchez: Hi, I am trying to run a SLAB of water with a solute and I want to put a wall on the z axis edge. My problem is

Re: [gmx-users] Keeping cis configuration of a molecule

On 2/26/18 7:28 AM, Anjana Jayasinghe wrote: Dear All, I want to keep the cis configuration of my molecule in MD simulation. How can I do that? Could you please help me? Likely you need a dihedral restraint. Refer to the manual. -Justin --

[gmx-users] Keeping cis configuration of a molecule

Dear All, I want to keep the cis configuration of my molecule in MD simulation. How can I do that? Could you please help me? Thank you. -- 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

Re: [gmx-users] g_sans calculation

The gmx sans and saxs tools are both using the Debeye formula to calculate scattering angles. In gmx sans it is possible to use a monte carlo method to limit the computational complexity of Debeye, which is O(n^2). On Fri, Feb 23, 2018 at 9:48 PM, João Henriques < joao.m.a.henriq...@gmail.com>

Re: [gmx-users] Positive potential energy

Hi, Thanks for your help, Justin! Regards, Mahsa On Sun, Feb 25, 2018 at 5:53 PM, Justin Lemkul wrote: > > > On 2/25/18 10:15 AM, Mahsa wrote: > >> Dear Justin, >> >> Thank you for your reply! >> >> In general, is it a good approach to first use steep algorithm for EM and >>