Re: [gmx-users] Positive potential energy

2018-02-26 Thread Mahsa
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 >>

Re: [gmx-users] g_sans calculation

2018-02-26 Thread Joe Jordan
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] About and index file of a monolayer...

2018-02-26 Thread Joe Jordan
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] cpu/gpu utilization

2018-02-26 Thread Mahmood Naderan
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

2018-02-26 Thread Adriaan Riet
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] cpu/gpu utilization

2018-02-26 Thread Szilárd Páll
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 >

Re: [gmx-users] residue error

2018-02-26 Thread Quyen V. Vu
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

2018-02-26 Thread Sankaran SV .
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] walls with slab of water

2018-02-26 Thread Jochen Hub
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

2018-02-26 Thread Justin Lemkul
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

2018-02-26 Thread Anjana Jayasinghe
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

[gmx-users] residue error

2018-02-26 Thread Radhika Arora
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] residue error

2018-02-26 Thread Justin Lemkul
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] About and index file of a monolayer...

2018-02-26 Thread Poncho Arvayo Zatarain
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