On 9/25/14 4:57 AM, marcello cammarata wrote:
Hi to all,
in order to find the position tangled of a polymer chain,
i tried to follow the indication of hte page Polymer reported in the gromacs
guide on line.
i created a file oplsaa.rtp and a file oplsaa.hdb as descrived there, and i
save t
Hi to all,
in order to find the position tangled of a polymer chain,
i tried to follow the indication of hte page Polymer reported in the gromacs
guide on line.
i created a file oplsaa.rtp and a file oplsaa.hdb as descrived there, and i
save the file on the folder oplsaa, also i created a file
On 9/23/14 7:43 PM, marcello cammarata wrote:
Do you know how change force field?
how i can do this?
Everything you need to create the polymer is described here:
http://www.gromacs.org/Documentation/How-tos/Polymers
The page includes a link to a discussion that goes step-by-step through how
arata
> Sent: Wednesday, 24 September 2014 9:43 AM
> To: Johnny Lu; gmx-us...@gromacs.org
> Subject: Re: [gmx-users] I: How to rolled up a polymer chain
>
> Do you know how change force field?
> how i can do this?
> so the goal can be this, i can consider two molecules asmetilene or
Do you know how change force field?
how i can do this?
so the goal can be this, i can consider two molecules asmetilene or ethilene or
butene, and i want kwon by appling a set of force field the mutual distance
beetween the two groups.
How i can do this?
how is possible to set force field?
bes
Molecular dynamics software, like gromacs, use a set of rules to simulate
the real world.
This set of rules is a force-field.
Force field is the simplified physical rules of the real world that are
hopefully approximately right.
Such simplified rules usually can not describe everything in the real
yes,
i need yto know how it go to tangled, related with the lenght of chain, the
number of chains in volume unit.
For now the problem is that when i run pdd2gmx, i don't choose any solvent,
because there isn't eny solvent, i choose only a kind of force field present in
the database software. b
Can I ask you something. What do you mean by "rolled up"? Do you mean create
the tangled conformation of polymer chains?
--Farid
22.09.2014, 20:46, "marcello cammarata" :
> Hi,
> i had checked all the archives, i have read about 100posts in the last 2
> month.
> Nobody have problem similar t
Hi. I noticed mis-spellings in manual of another MD software that persisted
throughout its versions.
Googling for "polyethylene simulation" gave this article as first result:
http://arxiv.org/pdf/1401.4295v1.pdf, which use lammps.
I'm not sure about the availability, accuracy, and computation cost
On 9/22/14 8:46 AM, marcello cammarata wrote:
Hi,
i had checked all the archives, i have read about 100posts in the last 2
month.
Nobody have problem similar to mine.
Problem for me are Two.
1- instead i am a doctor, i am not able to find the right advice at your site.
2- In your site there
Add the parameters for LIG residue in force filed. In that give information
about the LIG in
rtp file
nonbonded file
bonded file
I think then it will work.
On Mon, Sep 22, 2014 at 5:46 AM, marcello cammarata
wrote:
>
> Hi,
> i had checked all the archives, i have read about 100posts in the last
Hi,
i had checked all the archives, i have read about 100posts in the last 2 month.
Nobody have problem similar to mine.
Problem for me are Two.
1- instead i am a doctor, i am not able to find the right advice at your site.
2- In your site there is no space for begginer user.
The main pages w
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