Hi,
this is problem regarding g_mmpbsa
your not provided required information such as Gromacs version and g_mmpbsa
installation from source or binary ?!
in common if you using Gromacs 5.1.1 install g_mmpbsa from binary package
instead of compiling from source
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Dear all,
we would like to purchase one GPU enabled workstation system for molecular
dynamics work,we will be running mainly GROMACS, NAMD and CHARMM (older
version which do not support GPU)
i welcome suggestions regarding the below configurations
kindly provide your valued suggestions
Like re
Dear Gromacs users
I am doing an mm_pbsa analysis of my protein-ligand complex. I installed
and it was nicely running on my workstation Z820. However, on a similar
system, i installed using same steps but it is giving following error:
*Not enough memory. Failed to calloc -1082130432 elements of
On 3/21/16 1:29 PM, gozde ergin wrote:
Ok this was a silly question.
In g_energy command 5. one is flat-bottom posres force.
Sorry.
The output of g_energy is energy, not force.
But the quantity is simple to calculate. If you have applied a flat-bottom
restraint along z, then you just need
Ok this was a silly question.
In g_energy command 5. one is flat-bottom posres force.
Sorry.
> On 21 Mar 2016, at 17:26, gozde ergin wrote:
>
> Hey Justin,
>
> I am just wondering in order to estimate the osmotic pressure I need extract
> the flat-bottom restraint force. (Force/Area = Pressur
Hey Justin,
I am just wondering in order to estimate the osmotic pressure I need extract
the flat-bottom restraint force. (Force/Area = Pressure)
Do you have any idea to how to extract this force?
Thanks in advance
> On 10 Mar 2016, at 15:58, Justin Lemkul wrote:
>
>
>
> On 3/10/16 4:44 A
Dear Justin
I want to study the filctuation of dipole moment near surface of
CNT surrounded by water
I want to peculiarly choose water molecules covering certain distance . how to
choose such water molecules?
With high regardsS.Vidhyasankar
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On 3/21/16 8:03 AM, xy21hb wrote:
Hi Justin,
Thanks for your quick reply. But I came across some paper about the topic,
it seems that the simulation is not that just to change the temperature,
http://scitation.aip.org/docserver/fulltext/aip/journal/jcp/112/10/1.481085.pdf?expires=1458561931&id
Hi Justin,
Thanks for your quick reply. But I came across some paper about the topic,
it seems that the simulation is not that just to change the temperature,
http://scitation.aip.org/docserver/fulltext/aip/journal/jcp/112/10/1.481085.pdf?expires=1458561931&id=id&accname=2256636&checksum=B606E2B28
On 3/21/16 7:12 AM, xy21hb wrote:
Dear all,
I am following the gromacs tutorial for lipid bilayer,
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/06_equil.html
and wondering how I could simulate the gel phase (not the phase transition from
liquid phas
Dear all,
I am following the gromacs tutorial for lipid bilayer,
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/06_equil.html
and wondering how I could simulate the gel phase (not the phase transition from
liquid phase to gel phase) in this ca
Dear all,
I am following the gromacs tutorial for lipid bilayer,
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/06_equil.html
and wondering how I could simulate the gel phase (not the phase transition from
liquid phase to gel phase) in this case as a co
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