[gmx-users] Structure factor and scattering intensity in gromacs 5.1.4

Dear All, How to calculate structure factor and scattering intensity in gromacs 5.1.4. Thanks, Rakesh Sent with Mailtrack

Re: [gmx-users] request

What is -s md ? in the command line. On 05-Dec-2017 12:32 AM, wrote: hi.what causes this error? Command line: gmx mdrun -s md -cpi md_0_1_prev.cpt Output file appending has been requested, but some output files listed in the checkpoint file md_0_1_prev.cpt are not

Re: [gmx-users] Regarding use of g_x2top utility in Gromacs

to make it work correctly. Good luck. -Alex On 26/11/2017 10:52, Rakesh Pant wrote: > Dear, Alex > Does it mean, we do not need to define all the atomtypes in the .nt2 file. > It is enough to define all types in bonded and non-bonded itp. > > Thanks, > Rakesh > > > &g

Re: [gmx-users] Regarding use of g_x2top utility in Gromacs

5725 ; H-O-C > Hydrogen; > > > You would need to search literature for respective ff parameters: all the > above parameters are taken from another topology to give a template. > > > -Alex > > > On 26/11/2017 10:37, Rakesh Pant wrote: > >> Dear Alex, >>

Re: [gmx-users] Regarding use of g_x2top utility in Gromacs

gen > > ... > > Then you need *.n2t file in your ff. > > Good luck! > > > -Alex > > > On 25/11/2017 22:06, Justin Lemkul wrote: > >> >> >> On 11/25/17 3:31 PM, Rakesh Pant wrote: >> >>> But then I how will include the C atom (which i

Re: [gmx-users] Regarding use of g_x2top utility in Gromacs

.@vt.edu> wrote: > > > On 11/25/17 3:21 PM, Rakesh Pant wrote: > >> Dear Justin, >> >> I am trying to use it for graphene oxide (layer), then what would be a >> better way if not g_x2top. >> > > Epoxide O and phenolic O have different connectivity (t

Re: [gmx-users] Regarding use of g_x2top utility in Gromacs

7 at 1:48 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 11/25/17 3:12 PM, Rakesh Pant wrote: > >> Dear All, >> >> How does the utility g_x2top works? >> If we have similar connectivity in a molecule, then how will it read >> different atom types. Suppo

[gmx-users] Regarding use of g_x2top utility in Gromacs

Dear All, How does the utility g_x2top works? If we have similar connectivity in a molecule, then how will it read different atom types. Suppose a C atom is connected to 4 bonds (3 carbon atoms and 1 O atom, say in epoxy group) and similarly another C atom is also connected to 4 atoms (3 C atoms

[gmx-users] Doubt from Graphene oxide layer

Hi, I want to create a Graphene Oxide (GO) layer using some computational tools. It consists of different type of functional groups like hydroxy, carboxylic, and epoxy. VMD can generate Graphene layer. How Can I generate GO layer by using some computational tools? Thanks -- Rakesh Pant/राकेश

Re: [gmx-users] Doubt from force constant calculations

Dear Justin, Could you briefly tell how the vibrational analysis is done. Which method and software is generally used. Thanks Rakesh On Fri, Mar 17, 2017 at 7:16 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 3/17/17 7:53 AM, Rakesh Pant wrote: > >> Dear all, >

[gmx-users] Doubt from force constant calculations

Dear all, How to calculate force constant for bonds and angles using quantum chemistry calculations. Thanks Rakesh -- 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

Re: [gmx-users] Doubt from topology creation

lem...@vt.edu> wrote: > > > On 2/21/17 10:05 AM, Rakesh Pant wrote: > >> Dear all, >> >> I am trying to create a topology for a molecule using g_x2top and have >> defined all the atoms with connectivity in *atomname.n2t* file with >> different opls no.

[gmx-users] Doubt from topology creation

opls no. for some of the atoms. I have attached the pdb file and .n2t file. Thanks -- Rakesh Pant/राकेश पंत Research Fellow/अनुसंधान फेलो Indian Institute of Science Education and Research (IISER) भारतीय विज्ञान शिक्षा एवं अनुसंधान संस्थान Pune-411008, India/ पुणे - ४११००८, भारत Web:http

[gmx-users] Doubt from topology creation using g_x2top

Dear all, I am trying to create a topology for a molecule using g_x2top and have defined all the atoms with connectivity in *atomname.n2t* file with different opls no. for all different types of atoms. But when I create topology, it does not identify all different atomtypes and takes one common