Re: [gmx-users] Cross-linking of polymers

Dear Dr. Warren: Thank you for your answer and sorry for my ignorantness. I will do more literature survey... Thank you again. Sincerely, Kim On Sun, Mar 22, 2009 at 11:30 PM, Dallas B. Warren < dallas.war...@pharm.monash.edu.au> wrote: > Kim, > > >Recently I have been focusing on cross-lin

[gmx-users] Cross-linking of polymers

Dear All: I appreciate your care and help all the time. As you may know I am trying to simulate polymer behaviors. Recently I have been focusing on cross-linking phenomenon of polymers. As far as I understood, cross-linking include bond breaks in one polymer chain and bond occurrences among broke

Re: [gmx-users] Matching atom name and types in OPLS-aa FF

Dear Dr. Periole: Thank you for your answer. That was the point which I wanted to double check (of course after reading the manual...). Thank you again! Sincerely, Kim On Tue, Mar 17, 2009 at 6:09 PM, XAvier Periole wrote: > > On Mar 17, 2009, at 8:45 AM, tree wrote: > >

Re: [gmx-users] Matching atom name and types in OPLS-aa FF

[can I use the Forth power potential for bond strech using the given OPLS-aa paramters?] I assume this would be same to others, angle, dihedral, and etc. Thank you again. Sincerely, Kim On Mon, 16 Mar 2009, Justin A. Lemkul wrote: Tree wrote: Dear Dr. Periole: Thank you for your a

Re: [gmx-users] Matching atom name and types in OPLS-aa FF

16, 2009 at 5:42 PM, XAvier Periole wrote: > > On Mar 16, 2009, at 9:34 AM, tree wrote: > > Dear Justin and All: >> >> >> I truly appreciate your clear answer. >> Since my questions are solved by your explanations, I do not know how I >> can express my

Re: [gmx-users] Matching atom name and types in OPLS-aa FF

the bonds (strech) between two bonds is used. If this is Gromos potential, I am sure this "1" means "harmonic" potential according to the Chap. 4 of the Gromacs manual. Is this also applied to OPLS-aa FF? Thank you for your care, again. Sincerely yours, Kim On Fri, 13 Mar

[gmx-users] Fwd: Matching atom name and types in OPLS-aa FF

Since I cannot see my message on the gmx-users mail list, I am forwarding this again.I am sorry to bother your email box again... Hope you would understand... -- Forwarded message -- From: Tree Date: Fri, Mar 13, 2009 at 8:51 PM Subject: Matching atom name and types in OPLS-aa

[gmx-users] Matching atom name and types in OPLS-aa FF

Dear All: I appreciate your answer always. Right now, I am trying to add/modify some values in OPLS-aa FF. I am confused atom type (opls_xxx) and atom name (e.g., C) in "atp", "bon.itp", and "nb.itp" files. Please let me try the situation by an example, first. In "atp" file, ... opls_058

[gmx-users] Fwd: Force Field - Gromos96

-- Forwarded message -- From: tree Date: Thu, Mar 12, 2009 at 10:09 PM Subject: Force Field - Gromos96 To: gmx-users@gromacs.org Dear All: I appreciate it if it would be possible for me to have an answer related to Gromos96 force field. I am hoping to know if the Gromos96

[gmx-users] Force Field - Gromos96

Dear All: I appreciate it if it would be possible for me to have an answer related to Gromos96 force field. I am hoping to know if the Gromos96 force field can support All-Atom calculation? (Or does it 'only' support Unified Atom simulation?) Thank you for your care! Sincerely, C Kim __

Re: [gmx-users] Polymer entanglement simulation

y Justin, I will change mdp file and increase the time duration. If I get a good(?) result, I will post-! Thank you so much. Sincerely yours, Chansoo On Sat, Mar 7, 2009 at 5:45 PM, Justin A. Lemkul wrote: > > > Mark Abraham wrote: > >> - Original Message - >> Fro

Re: [gmx-users] Polymer entanglement simulation

= all-bonds Ends Thank you, always! Sincerely, C. Kim On Sat, Mar 7, 2009 at 2:19 PM, Justin A. Lemkul wrote: > > > Tree wrote: > >> Dear Users: >> >> >> Hello? >> As you might know, I am trying to simulate polymer chains with gromacs. &g

[gmx-users] Polymer entanglement simulation

Dear Users: Hello? As you might know, I am trying to simulate polymer chains with gromacs. Thanks to Justin's large help, I can build topology, which is the essential to actually run the MD. After getting the MD result, I have a serious question. For polymer, as same as the other biopolymers, I a

Fwd: [gmx-users] How to define "stretch" in ffoplsaabon.itp ?

ation from oplsaa.rtp and opls*.itp. Thank you! Sincerely yours, C Kim -- Forwarded message -- From: Tree Date: Wed, Mar 4, 2009 at 10:11 AM Subject: Re: [gmx-users] How to define "stretch" in ffoplsaabon.itp ? To: Discussion list for GROMACS users Dear Justin: O

Re: [gmx-users] How to define "stretch" in ffoplsaabon.itp ?

Dear Justin: On Wed, Mar 4, 2009 at 10:04 AM, Justin A. Lemkul wrote: > > > Tree wrote: > >> Dear Justin: >> >> >> Thank you for your answer!! >> Yes, I found there is already a bond defined for CT and CT, meanwhile I am >> waiting response fr

Re: [gmx-users] How to define "stretch" in ffoplsaabon.itp ?

"csoplsaanb.itp". Thank you again! Sincerely C Kim On Wed, Mar 4, 2009 at 9:47 AM, Justin A. Lemkul wrote: > > > Tree wrote: > >> Dear All: >> >> >> *[1 - Situation]* >> I am trying to define "stretch" between two bonded a

[gmx-users] Fwd: How to define "stretch" in ffoplsaabon.itp ?

In the section [3], the file is "csoplsaanb.itp". In the file, I found how an opls_xxx is assigned to an atom type. (If this is a CORRECT approach...) Thank you! Sincerely, C. Kim -- Forwarded message ------ From: Tree Date: Wed, Mar 4, 2009 at 9:38 AM Subject: How

[gmx-users] How to define "stretch" in ffoplsaabon.itp ?

Dear All: *[1 - Situation]* I am trying to define "stretch" between two bonded atoms (for example, in my system PE (polyethylene), C-C). *[2 - ffoplsaa.rtp file]* In ffoplsaa.rtp file, I assigned C1> opls_136 C2> opls_135 This can be done by my own idea, so it does not bothe