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
>> then to further mi
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> wro
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.
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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
--
==
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 h
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
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 1
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?
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Gromacs Users mailing li
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
molecules
> On Feb 26, 2018, at 10:31 AM, Joe Jordan wrote:
>
> 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 b
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
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 t
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
> input_md", I see that
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
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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 database.
> Please let me know how
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