Re: [gmx-users] I: How to rolled up a polymer chain

2014-09-25 Thread Justin Lemkul
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

Re: [gmx-users] I: How to rolled up a polymer chain

2014-09-25 Thread marcello cammarata
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

Re: [gmx-users] I: How to rolled up a polymer chain

2014-09-23 Thread Justin Lemkul
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

Re: [gmx-users] I: How to rolled up a polymer chain

2014-09-23 Thread Dallas Warren
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

Re: [gmx-users] I: How to rolled up a polymer chain

2014-09-23 Thread marcello cammarata
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

Re: [gmx-users] I: How to rolled up a polymer chain

2014-09-23 Thread Johnny Lu
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

Re: [gmx-users] I: How to rolled up a polymer chain

2014-09-23 Thread marcello cammarata
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

Re: [gmx-users] I: How to rolled up a polymer chain

2014-09-23 Thread Mohd Farid Ismail
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

Re: [gmx-users] I: How to rolled up a polymer chain

2014-09-22 Thread Johnny Lu
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

Re: [gmx-users] I: How to rolled up a polymer chain

2014-09-22 Thread Justin Lemkul
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

Re: [gmx-users] I: How to rolled up a polymer chain

2014-09-22 Thread Sathish Kumar
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

[gmx-users] I: How to rolled up a polymer chain

2014-09-22 Thread marcello cammarata
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