Re: [gmx-users] Gromacs tutorial

ww.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-user

[gmx-users] Generation of force field for "NME " capping group

field for "Nme" in gromos. Regards Nidhi -- 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 * For (un)subscribe requests v

[gmx-users] Query regarding capping group "NME"

Dear Gromacs users, I want to capped the end groups of a protein chain with acetyl (ACE) and amine (NME) groups. As I am using gromos96 43A1 force field and NMe is not present in aminoacid.rtp. In amber NME is present but not in gromos. Anyone please suggest something how to generate force

Re: [gmx-users] Doubt in nmol tool

Dhanyavad!! On Mon, 8 Apr 2019, 16:34 Soham Sarkar, wrote: > No need to use -nmol > > On Mon, 8 Apr 2019, 4:21 pm nidhi, wrote: > > > That means there is no need of using -nmol option. > > > > Thank You very much :) > > > > > > On

Re: [gmx-users] Doubt in nmol tool

That means there is no need of using -nmol option. Thank You very much :) On Mon, Apr 8, 2019 at 3:57 PM Soham Sarkar wrote: > In that case select all c-alpha and make a group in index.ndx and run gmx > gyrate for this group only and you are done. > > On Mon, 8 Apr 2019, 3:09 pm n

Re: [gmx-users] Doubt in nmol tool

I want to to calculate Rg of whole protein in the simulation box at a time not the individual chains. And for this I have selected Rg for "C-alpha" atoms plus "-nmol 3" . Thank You, Sundari On Mon, Apr 8, 2019 at 2:50 PM Soham Sarkar wrote: > What do you want? > Do you want to calculate the

Re: [gmx-users] Secondary structure content

I also have same doubt. On 9 Sep 2017 11:13 p.m., "nidhi" <nidhi020...@gmail.com> wrote: > Thank you :) > Can you please suggest me than what's the last line of scount.xvg file > indicates? > It is ss(%), what does it mean? Which kind of secondary structure > pe

Re: [gmx-users] Secondary structure content

Thank you :) Can you please suggest me than what's the last line of scount.xvg file indicates? It is ss(%), what does it mean? Which kind of secondary structure percentage is this? Thank you for your time and help.. On 9 Sep 2017 7:03 p.m., "Justin Lemkul" wrote: > > > On

Re: [gmx-users] Calculation of nematic order parameter using gromacs

Thank you all.. I am a newly research scholar that's why taking some time in understanding :) I will try again.. Nidhi On 3 Jun 2017 7:49 p.m., "André Farias de Moura" <mo...@ufscar.br> wrote: > Nidhi, > > you need some background reading on the specifics of your pr

Re: [gmx-users] Calculation of nematic order parameter using gromacs

In my case for second order parameter I need the angle between the unit vector linking N- and C-termini of the ith peptide and the d (the director) is a unit vector defining the preferred direction of alignment. These vectors are not clear to me.. please suggest something. Nidhi On Sat, Jun

Re: [gmx-users] Calculation of nematic order parameter using gromacs

Hello, Thank you Antonio.. But my angle of interest is the angle between the molecular axis of protein and the director. I am not able to understand here, from where I can choose this 'director'? Nidhi On 30 May 2017 8:55 p.m., "Antonio Baptista" <bapti...@itqb.unl.pt> wr

[gmx-users] Calculation of nematic order parameter using gromacs

Dear All, I want to calculate the nematic order parameter (p2) at each time step. Is it possible to do this with "gmx order"? If not than please suggest the right way. Thank you, Nidhi -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mai

[gmx-users] problem in parametrization of NH2 group

but don't know how to convert it to .rtp. Kindly help regarding this. Thanking you Yours sincerely -- Nidhi Batra DBT-Research Associate Institute of Genomics and Integrative Biology (IGIB), Mathura Road, Sukhdev Vihar New Delhi 110020 -- Gromacs Users mailing list * Please search the archive

[gmx-users] mean square displacement

. Thanks Nidhi -- 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 * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo

Re: [gmx-users] regarding MSD

getting the same transition temperature but the MSD values are coming different (eg at a particular temperature if I average all the MSD values, I am getting value of 15000 while reported value is 1.5 - both values in same unit angstrom square) On Fri, Aug 22, 2014 at 7:15 PM, Nidhi Katyal

Re: [gmx-users] regarding MSD

is highly appreciated. On Thu, Aug 21, 2014 at 9:56 PM, Nidhi Katyal nidhikatyal1...@gmail.com wrote: Hello all I have read few papers that determine transition temperature from the plot of average MSD versus temperature. My question is: At a particular temperature, we get a linear curve

[gmx-users] regarding g_hydorder

): #Legend #TBlock #Xbin Ybin Z t 0 0 0 6.5 0 1 6.5 0 2 4.5 0 3 3.5 0 4 6.5 0 5 4.5 0 6 5.5 1 0 6.5 1 1 4.5 1 2 5.5 1 3 3.5 1 4 5.5 1 5 4.5 1 6 5.5 2 0 4.5 . . Please help me in interpreting this file. Thanks Nidhi -- Gromacs Users mailing

[gmx-users] regarding MSD

that is plotted in papers (or something is missing) ? My doubt is won't this average depend on the number of time points (due to its linear nature)? Any help is highly appreciated. Thanks Nidhi -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support

Re: [gmx-users] atoms are not part of any of the T-Coupling groups

in advance. Nidhi On Wed, Aug 6, 2014 at 8:06 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/6/14, 3:46 AM, Nidhi Katyal wrote: Hello all, I am working on protein with two chains. I would like to restrain one atom of one chain while doing steered MD. For the same reason, I have created

[gmx-users] atoms are not part of any of the T-Coupling groups

the problem. Thanks Nidhi -- 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 * For (un)subscribe requests visit https://maillist.sys.kth.se

Re: [gmx-users] Groups in index.ndx

Use make_ndx -f *.gro -n old_index.ndx -o old_index.ndx On Fri, Jul 25, 2014 at 4:53 PM, INPE (Ingrid Viveka Pettersson) i...@novonordisk.com wrote: Dear Group, I have defined different specific groups in the index.ndx file. My problem is that if I try to add a new group, the old ones are

[gmx-users] Running job on GPUs

cores and GPUs? Thanks Nidhi -- 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 * For (un)subscribe requests visit https://maillist.sys.kth.se

[gmx-users] g_hbond

in the existence map created using hbm option, I could see 19 lines. But when I generate index file with a2 and calculate hydrogen bond with my ligand moleules, I can see zero bonds. Am I doing something wrong? Thanks Nidhi -- Gromacs Users mailing list * Please search the archive at http

[gmx-users] Hydrogen bond existence map

of simulation. Is it possible with gromacs? Thanks in advance Nidhi -- 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 * For (un)subscribe requests

[gmx-users] binding sites with MD

Hi all, I would like to ask if unbiased MD in nanoseconds time scale be used to find the potential binding sites of ligand with protein? I have simulated for 50ns, 1:14 and 1:24 protein:ligand simultaneously with random placement of ligand initially. In the time interval between 40 to 50ns,

Re: [gmx-users] parameters problem

at the moment, which would cause this problem. Mark On Mon, Mar 10, 2014 at 7:09 PM, Nidhi Katyal nidhikatyal1...@gmail.com wrote: To test swiss param parameters, I have generated *.pdb and *.itp files from it. In the genbox command, I have used -ci *.pdb -nmol 2. I have included *.itp

Re: [gmx-users] parameters problem

for directive atomtypes Please help me rectify the problem of the order getting violated although same worked for topology generated by PRODRG. Thanks in advance. On Mon, Mar 10, 2014 at 10:06 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/10/14, 8:21 AM, Nidhi Katyal wrote: Thanks Justin. I

[gmx-users] antiparallel beta sheet

as output and not through visual inspection)? Thanks in advance. Nidhi -- 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 * For (un)subscribe requests

[gmx-users] xpm2ps

. Nidhi -- 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 * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo

[gmx-users] parameters problem

Dear all I am trying to simulate a protein in 3 steps: energy minimization (using em.mdp), position restraints (using pr.mdp) and final production run by NPT ensemble (using full.mdp) at 300K At this temperature, it is known by previous literature survey that protein keeps its secondary

Re: [gmx-users] converting .xpm to .eps

, Nidhi Jatana nidhijat...@bic-svc.ac.in wrote: Dear Sir/Madam Please find attached the file containing the error. Thanking you Regards -- Nidhi Jatana Senior Research Fellow Bioinformatics Center Sri Venkateswara College (University of Delhi) Dhaula Kuan New Delhi-110021

Re: [gmx-users] converting .xpm to .eps

How do you fix the matrix size? Should I do it while generation of .xpm file or while converting it to .eps and using which option? Regards Nidhi On Fri, Dec 20, 2013 at 3:35 PM, Carsten Kutzner ckut...@gwdg.de wrote: On 12/20/2013 10:09 AM, bipin singh wrote: Not sure, might be something

[gmx-users] converting .xpm to .eps

. xpm2ps -f *.xpm -o *.eps -rainbow red -xpm *.xpm I have tried many options with setting -bx and -by but of no help. I also tried taking the .m2p file but the problem persist. Please find attached the .m2p file for reference. Please help me with this. Thanking you Regards -- Nidhi Jatana Senior