Re: [gmx-users] TFE-water simulation

Should I start with helical peptides and see if it maintains the helicity or I can start with random coil? Do random coil peptides take long simulation time to form helical peptides? any help on this will be appreciated. On Tue, Nov 5, 2013 at 12:25 AM, Archana Sonawani-Jagtap < ask.a

Re: [gmx-users] TFE-water simulation

Lund University > Lund, Sweden > ---- > joao.henriq...@teokem.lu.se > http://www.teokem.lu.se/~joaoh/ > > > On Thu, Oct 24, 2013 at 7:15 PM, Justin Lemkul wrote: > > > > > > > On 10/24/13 1:13 PM, Archana Sona

Re: [gmx-users] TFE-water simulation

de me some hint? Is their need to remove periodicity of this pre-equilibrated system as in case of lipids? Regards, Archana On Wed, Oct 23, 2013 at 5:26 PM, Justin Lemkul wrote: > > > On 10/23/13 7:20 AM, Archana Sonawani-Jagtap wrote: > >> Hi all, >> >> I have n

[gmx-users] TFE-water simulation

is welcome. Thank you. -- Archana Sonawani-Jagtap Senior Research Fellow, Biomedical Informatics Centre, NIRRH (ICMR), Parel Mumbai, India. 9960791339 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http

Re: [gmx-users] Bilayer thickness error

thank you so much. It was such a stupid error from my side. On Fri, Oct 18, 2013 at 5:08 PM, Justin Lemkul wrote: > > > On 10/18/13 2:54 AM, Archana Sonawani-Jagtap wrote: > >> Hi, >> This is my input file for calculating bilayer thickness in absence of >> pep

[gmx-users] Bilayer thickness error

without peptide) When running in Gnuplot I get following error: splot 'output.frame1.20x20.average_thickness.dat' matrix using (1+$1):(1+$2):3 Warning: empty x range [1:1], adjusting to [0.99:1.01] Please help me. -- Archana Sonawani-Jagtap Senior Research Fellow, Biomedical Informat

[gmx-users] (no subject)

l be printed to output.frame1.200x198.bottom_a reas.dat -- Archana Sonawani-Jagtap Senior Research Fellow, Biomedical Informatics Centre, NIRRH (ICMR), Parel Mumbai, India. 9960791339 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Pl

[gmx-users] lipid tail order

same manner as Justin's KALP tutorial skipping the peptide insertion part? Please help me... thanks in advance -- Archana Sonawani-Jagtap Senior Research Fellow, Biomedical Informatics Centre, NIRRH (ICMR), Parel Mumbai, India. 9960791339 -- gmx-users mailing listgmx-users@gromac

[gmx-users] Bilayer thickness

the lateral area of system and APL.(keeping thickness as no) which lateral area has to be considered as the thickness of the bilayer in terms of nm? both have different values. I am confused. which values should be reported for thickness and APL? Please help me. -- Archana Sonawani-Jagtap

Re: [gmx-users] pair distribution function

Thank you. On Sun, Oct 6, 2013 at 8:12 PM, Justin Lemkul wrote: > > > On 10/6/13 10:36 AM, Archana Sonawani-Jagtap wrote: > >> I have simulations for different peptides in POPC bilayer. >> >> I want to calculate pair distribution function (pdf) between negativel

[gmx-users] pair distribution function

calculate the center of mass for a bilayer? Any help is highly appreciated. -- Archana Sonawani-Jagtap Senior Research Fellow, Biomedical Informatics Centre, NIRRH (ICMR), Parel Mumbai, India. 9960791339 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx

Re: [gmx-users] TFE-water simulation

other mentioned steps. Thanks in advance. On Wed, Jul 17, 2013 at 2:41 PM, Justin Lemkul wrote: > > > On 7/17/13 1:03 AM, Archana Sonawani-Jagtap wrote: >> >> HI, >> >> I want to simulate helical peptide in TFE-water (1:1 vol) solvent. >> >> 1. From previo

[gmx-users] TFE-water simulation

-equilibrated system from ATB site. I dont know if I can use either this pdb or gro file during genbox step for -cs flag Can anyone help me out in this regard. Thanks in advance. Regards, Archana Sonawani-Jagtap Senior Research Fellow, Biomedical Informatics Centre, NIRRH (ICMR), Parel Mumbai, India