Re: [gmx-users] Surface tension

e surface tension itself, > which is not the case for most force fields). > > I hope it helps > > Andre > > On Tue, May 10, 2016 at 3:14 PM, Ganesh Shahane <ganesh7shah...@gmail.com> > wrote: > > > Dear Gromacs Users, > > > > I have been trying

[gmx-users] Surface tension

all the frames? Any help would be appreciated. Thank you! -- Cheers! Ganesh Shahane -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Topology for Sphingomyelin

Shahane <ganesh7shah...@gmail.com> wrote: > Thank you for your reply Justin!. It was helpful. > > On Fri, Jan 22, 2016 at 2:41 PM, Justin Lemkul <jalem...@vt.edu> wrote: > >> >> >> On 1/22/16 8:51 AM, Ganesh Shahane wrote: >> >>> Dear Gromac

[gmx-users] Topology for Sphingomyelin

in residue topology database of Charmm36 ff. Does anyone has any idea about where can I get topology for PSM? Or would it be wise to submit it to paramchem to get its topology? Thank you in advance. -- Best Regards, Ganesh Shahane -- Gromacs Users mailing list * Please search the archive at http

Re: [gmx-users] Topology for Sphingomyelin

Thank you for your reply Justin!. It was helpful. On Fri, Jan 22, 2016 at 2:41 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 1/22/16 8:51 AM, Ganesh Shahane wrote: > >> Dear Gromacs users, >> >> I wish to simulate a mixed lipid bilayer of which one of

[gmx-users] Simulations of inorganic polymers

Dear Gromacs Users, I need to simulate a specific polymer which consists of carbon, hydrogen and fluorine atoms. Could anyone please suggest some force fields for simulating inorganic polymer molecules that have been ported to gromacs? Thank you. -- Best Regards, Ganesh Shahane -- Gromacs

[gmx-users] Backmapping of POPE

coordinates for atom H91 of residue POPE. On checking the pope.charmm36.map file in Mapping folder, the atom H91 can be seen to be well defined in the bead D3B. Can anybody explain as to why it's throwing the error? Thank you. -- Best Regards, Ganesh Shahane -- Gromacs Users mailing list * Please

[gmx-users] POPC simulation with heavy hydrogens and 4 fs timestep

very dynamic, start "freezing" as the KE approaches zero. Does anybody has any idea as to where I am going wrong? Thank you. -- Best Regards, Ganesh Shahane -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before pos

Re: [gmx-users] trjconv -pbc nojump

equests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Best Regards, Ganesh Shahane -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_L

Re: [gmx-users] Few queries about microsecond long simulations

, Ganesh Shahane ganesh7shah...@gmail.com wrote: Hi Anu, 1) It really depends on what kind of analysis you are doing. If you are, for example, studying bio-molecular interactions that take place over microsecond long timescales then saving trajectories every 200-500 ps is advisable

Re: [gmx-users] Few queries about microsecond long simulations

://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Best Regards, Ganesh Shahane -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post

Re: [gmx-users] Topology file for serotonin (5-HT)

of these dihedrals? Thanks! On Mon, Jul 27, 2015 at 5:43 AM, Justin Lemkul jalem...@vt.edu wrote: On 7/23/15 2:10 AM, Ganesh Shahane wrote: Dear Gromacs Users, I am looking forward to performing some simulations of a receptor bound to serotonin (also known as 5-HT). Does anybody have the .itp file

[gmx-users] Topology file for serotonin (5-HT)

Dear Gromacs Users, I am looking forward to performing some simulations of a receptor bound to serotonin (also known as 5-HT). Does anybody have the .itp file of serotonin for the charmm27 or charmm36 force field? Thank you! -- Best Regards, Ganesh Shahane -- Gromacs Users mailing list

Re: [gmx-users] g_msd and Diffusion Constant

are meaningful If I got this situation, I would report 10^(-8)cm^2/s. On Tue, Jul 21, 2015 at 2:14 AM, Ganesh Shahane ganesh7shah...@gmail.com wrote: Hi! I am using gromacs version 4.5.5. The values are different. The value displayed on the terminal screen is 0.0007417*1e-5 cm^2/s while

Re: [gmx-users] g_msd and Diffusion Constant

AM, Ganesh Shahane ganesh7shah...@gmail.com wrote: Hi! I am using gromacs version 4.5.5. The values are different. The value displayed on the terminal screen is 0.0007417*1e-5 cm^2/s while the value displayed in the chol.xvg file is 0.000903331*1e-5 cm^2/s. As you can see, both

[gmx-users] g_msd and Diffusion Constant

be taken as the value of diffusion constant? Any help would be appreciated. Thank you! -- Best Regards, Ganesh Shahane -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http

Re: [gmx-users] g_msd and Diffusion Constant

, V.V.Chaban vvcha...@gmail.com wrote: which version fo you use? On Mon, Jul 20, 2015 at 8:28 AM, Ganesh Shahane ganesh7shah...@gmail.com wrote: Dear Gromacs Users, I have performed a simulation of a POPC+Cholesterol bilayer. I wish to know the diffusion constant of a particular