[gmx-users] Please give me advises for the computing system.

d for Gromacs? (I heard that i7 work well in some simulation but not sure of Gromacs) Thank you a lot! Sincerely, Seungpyo Hong -- -- 'God used beautiful mathematics in creating the world.' -Paul Dirac 'At the same time, he allowed inter

[gmx-users] Positive energy for Coulumb term. Does this mean Coulumb interaction destabilizes protein?

ion or comment would be great help for me. Thank you very much! Sincerely, Seungpyo Hong -- -- 'God used beautiful mathematics in creating the world.' -Paul Dirac 'At the same time, he allowed interaction among objects.' -Seungpyo

Re: [gmx-users] Re: Positive energy for Coulumb term. Does this mean Coulumb, interaction destabilizes protein? (Seungpyo Hong)

Dear Gerrit, Thanks for your kind reply! I just forget covalent bonds! Best regards, Seungpyo Hong On Fri, Mar 6, 2009 at 8:05 PM, Gerrit Groenhof wrote: > Coulomb 1-4 is only beteen the atoms that are 3 bonds away from each other. > The bonds prevent these atoms to get apart too far,

[gmx-users] Please let me know where can I found parameters for Phosphorylated amino acids.

topologies, for the phosphorylated amino acid. Sincerely Seungpyo Hong. -- -- 'God used beautiful mathematics in creating the world.' -Paul Dirac 'But he created too many objects.' -Seungpyo Hong Seungpyo Hong Master stu

[gmx-users] Range checking error

hematics in creating the world.' -Paul Dirac 'But he created too many objects.' -Seungpyo Hong Seungpyo Hong Master student at PBIL(Protein BioInformatics Lab.) in KAIST, Daejeon Korea Tel. (82)-18-372-2468 [EMAIL PROTECTED] [EMAIL PROTECTED] __

[gmx-users] Loop displacement calculation?

'God used beautiful mathematics in creating the world.' -Paul Dirac 'But he created too many objects.' -Seungpyo Hong Seungpyo Hong Master student at PBIL(Protein BioInformatics Lab.) in KAIST, Daejeon Korea Tel. (82)-18-372-2468 [EMAIL PR

Re: [gmx-users] Loop displacement calculation?

code really calculate the free energy a certain ensenble of microstates, it can be used to test the stability of the part of the protein. On Tue, Apr 22, 2008 at 2:50 PM, Mark Abraham <[EMAIL PROTECTED]> wrote: > SeungPyo Hong wrote: > > > Dear gmx-users, > > (This is no

Re: [gmx-users] Loop displacement calculation?

Thank you very much Mark~ On Tue, Apr 22, 2008 at 4:27 PM, Mark Abraham <[EMAIL PROTECTED]> wrote: > SeungPyo Hong wrote: > > > Thank you for your kind response. > > > > I think that I do not clearly describe the system. > > > > The loop I mentioned ab

[gmx-users] gmxtest, error during pdb2gmx step.

matics in creating the world.' -Paul Dirac 'But he created too many objects.' -Seungpyo Hong Seungpyo Hong Master student at PBIL(Protein BioInformatics Lab.) in KAIST, Daejeon Korea Tel. (82)-18-372-2468 [EMAIL PROTECTED] [EMAIL PROTECTED] ___

[gmx-users] Applying constant force between two atoms

Dear gmx-users, I want to apply constant force between two atoms within a protein. But unfortunately I cannot find how to apply constant force. Would anybody talk me how to do it? Thanks, Seungpyo ___ gmx-users mailing listgmx-users@gromac

Re: [gmx-users] Applying constant force between two atoms

Thank you for paying attention. Maybe I have to study much more about Gromacs. ^^; Seungpyo On 7/2/07, Mark Abraham <[EMAIL PROTECTED]> wrote: > Dear gmx-users, > > > > I want to apply constant force between two atoms within a protein. > > But unfortunately I cannot find how to apply constant

[gmx-users] Implicit solvent simulation

Dear gmx-users, Recently I want to perform MD for protein with implicit solvent model. Gromacs does not seem to support it. Could you let me know where to find information about implicit solvent simulation with Gromacs? Also I will be glad if you tell me your opinion about the implicit solvent si

Re: [gmx-users] Implicit solvent simulation

Thank you for your kind reply, Stephane. Anyhow it is a little disappointing that Generalized-Born is not implemented in Gromacs. Sincerely, Seungpyo Hong On 7/16/07, Stéphane Téletchéa <[EMAIL PROTECTED]> wrote: SeungPyo Hong a écrit : > Dear gmx-users, > > Recently I want to

Re: Re: [gmx-users] number of coordinates in coordinate file does not match topology

he name in coordinate file? If not, it is better to math them. 3. Or, rewrite .mpd file with Linux editor. I don't know much about Linux. But when I rewrite .mpd file again it works. Seungpyo Hong On 7/24/07, Moore, Jonathan (J) <[EMAIL PROTECTED]> wrote: Christopher, I'm afraid I

[gmx-users] GROMACS vs. AMBER speed comparison?

reated too many object.' -Seungpyo Hong Seungpyo Hong Master student at PBIL(Protein BioInformatics Lab.) in KAIST, Daejeon Korea Tel. (82)-18-372-2468 [EMAIL PROTECTED] [EMAIL PROTECTED] ___ gmx-users mailing listgmx-users@gromacs.org http://www

Re: [gmx-users] energy minimization using double precision gromacs failed

e archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- -

Re: [gmx-users] GROMACS vs. AMBER speed comparison?

.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- -- 

Re: [gmx-users] hi

.gro) file and its .itp file might be helpful. When using Dundee server they give you the .gro file with all the hydrogen bound. But they give you 3 .pdb file. -- ------ 'God used beautiful mathematics in creating the world.' -Paul Dirac 'Bu

Re: [gmx-users] Ionic liquids

is eager to do it. I try to make the solvent by placing the molecules in lattice and run MD under pressure coupling. Though I am also a beginner in this field, I am not sure of the plausiblity of this method but it seems to be OK to me. -- -- 'God us

[gmx-users] Can I convert Amber (.prepin) into Gromacs (.itp) topology?

s has tool that generate topology parameters like antechamber in amber? Thank you for reading. -- -- 'God used beautiful mathematics in creating the world.' -Paul Dirac 'But he created too many objects.' -Seungpyo Hong Seungp

Re: [gmx-users] Ionic liquids

__ > Sampo Karkola > Doctoral student > > Laboratory of Organic Chemistry > Department of Chemistry > POBox 55, FIN-00014 > University of Helsinki > Finland > > tel. +358 9 19150369 > fax. +358 9 19150366 > [EMAIL PROTECTED] > > SeungPyo Ho

Re: [gmx-users] Can I convert Amber (.prepin) into Gromacs (.itp) topology?

Thank you very much Florian! It is what I want to know and I can successfully transform from amber format to gromacs format! Sincerely, Seungpyo Hong On 8/22/07, Florian Haberl <[EMAIL PROTECTED]> wrote: > > Hi, > > On Tuesday, 21. August 2007 22:14, SeungPyo Hong wrote:

[gmx-users] extract water coordinate from xtc

-- -- 'God used beautiful mathematics in creating the world.' -Paul Dirac 'But he created too many objects.' -Seungpyo Hong Seungpyo Hong Master student at PBIL(Protein BioInformatics Lab.) in KAIST, Daejeon Korea Tel. (82)-18-372-2468 [EMAIL PROTECT