[gmx-users] parameterization of new metal ion

hello sir, thanks for your kind reply.. while setting new parameters for metal ion NI2+ i edited my ions.itp by including the following lines.. [ moleculetype ] ; molname nrexcl NI 1 [ atoms ] ; idat type res nr residu name at name cg nr charge mass 1 NI2+1

[gmx-users] nvt equilibration output

Respected sir, thanks for your kind reply... i applied position restrain during nvt step sir.. Thanking you, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search b

[gmx-users] nvt equilibration output

Respected sir, I am studying about micelle formation .. After setting box and adding water i went for energy minimization and then went for nvt equilibration for 1ns. when i visualized my nvt.pdb file, i found that my protein comes together and formed three micelle like structure. but my box go

[gmx-users] regarding micelle index group

hello sir, Thanks a lot for your help.. i got my own index file for my micelles using make_ndx.. Thanking you, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search

[gmx-users] regarding micelle and its analysis - index group

hello sir, thanks for your kind reply.. i like to know how to calculate index groups for my micelles.. since i am having two micelles , one having 8molecules and another having 2molecules.. residue number for that 2molecule micelle is 2 and 7.. can you help me how to form index group for this t

[gmx-users] regarding micelle and its analysis

hello sir, i am studying about micelle formation of surfactants. i performed my run for 10ns.. when i visualize my final md pdb file i got around 2 to 3 micelles. my doubt is while performing analysis , g_gyrate giving a value of around 3nm.. this value corresponds to which micelle.. how its ca

[gmx-users] regarding g_sas and rdf

hello sir, thanks for your kind reply... to study about micelle formation is it correct to use g_polystat. to measure gyrate... also i tried g_sas to find the solvent accessible surface and g_rdf.. but i dono how to interpret the result from the graph.. i gave calculation group and output grou

[gmx-users] regarding potential energy positive

hello sir, Thanks a lot for your reply... now i am clear with my potential energy.. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don'

[gmx-users] regarding em potential energy positive

hello sir, initially i did dynamics for my protein with 3water molecules.. it went correctly.. when i thought of reducing water i decreased my box size so that my sol number is around 7. when i go for energy minimisation i got its output.. but when i analysed its potential energy its co

[gmx-users] regarding rmsd value

hello sir, Thanks for your kind reply... my extended simulation for additional 10ns is completed and when i analysed its rmsd its showing random variation.. i am trying to form micelle.. maybe this is the reason for this random variation... suppose if i extend my simulation further, maybe is it

[gmx-users] extending simulation

hello sir,, initially i did my simulation for 10ns.. after getting result i analysed it and thought of extending the simulation for another 10ns.. i used following commands.. tpbconv *-s md.tpr -o newmd.tpr -extend 1.00* *mdrun -s newmd.tpr -o md3_2.trr -c md_2.gro -e md_2.edr -g md_2.log -

[gmx-users] md step fragmentation

hello Mark sir, thanks a lot for your reply.. ya now i got full structure because of pbc. Thanking you, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before

[gmx-users] md step- structure fragmentation

hello sir, I performed simulation for 30ns, because of queue time limit my run terminated at 11.6ns.. i thought of analysing my trajectory file.. so generated pdb file from trr using dump option.. when i visualize the pdb,i noted that my protein structure got fragmented.. when i visualize my np

[gmx-users] mdrun extension and concatenation

hello sir, while performing simulation for 30ns, because of queue time limit my run terminated at 11.6ns.. then i extended my simulation using mdrun as you suggest.. while doing so i got error as Fatal error: Failed to lock: md20.log. Function not implemented. For more information and tips for t

[gmx-users] Re: gmx-users Digest, Vol 94, Issue 159

hello sir, Thanks for your kind reply.. i tried like what you suggest.. i used the command mdrun -s md60.tpr -cpi state.cpt -o md60.trr -x traj.xtc -e md60.edr -c md60.gro -g md60.log to extend my simulation.. but again i got error as follows Reading file md60.tpr, VERSION 4.5.5 (single pre

[gmx-users] Re: gmx-users Digest, Vol 94, Issue 159

hello sir, Thanks for your kind reply.. one small doubt sir.. its enough to give* mdrun -s md.tpr -cpi state.cpt * so that it ll automatically append my new data to the respective file .. Thanking you, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo

[gmx-users] extending a simulation after it get stopped because of queue time limit

hello sir, i was performing simulation for 30ns. due to queue time limit my mdrun stopped at 11.6ns.. then i extended my simulation using these two commands *tpbconv -s md.tpr -extend 2 -o newmd.tpr mdrun -s newmd.tpr -o md.trr -c md.gro -e md.edr -g md.log -cpi state.cpt -x traj.xtc -append

[gmx-users] regarding boxtype and numer of solvent molecules..

hello sir, Thanks for your kind reply.. 15 boxtype accomodates 105046 solvent molecules.. but i need to run simulation by keeping number of water molecules constant and changing number of protein molecules.. thanking you, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.

[gmx-users] regarding box dimension and number of solvent molecules

hello sir, i like to know few informations regarding box dimension and setting no.of.solvent molecules.. i want to run simulation for different number of protein molecules with same number of water molecules.. i used following commands to increase the no.of molecules i used genbox -nmol 100 -ci

[gmx-users] regarding rmsd plot obtained for less time

hello sir, I did dynamics for 5ns for my protein. i submitted my run in cluster.. i got my output.. when i go for rmsd and gyrate analysis i got plot for only 1.2ns out of 5ns.. i dono what is the problem.. is this because of low runtime in cluster.. even i gave 200hours in cluster.. i searched

[gmx-users] regarding nvt

hello sir, Thanks for your reply. Intensionally i didnt neutralise my system.. i am using version 3.3.3.. i like to know is there anything wrong in using maxwarn in my commamd? did maxwarn ll affect my result sir ? Thanking you, -- gmx-users mailing listgmx-users@gromacs.org http://lists

[gmx-users] regarding NVT

hello sir, Thanks for your reply initially i tried with v-rescale i am getting error.. now again i tried .. when i tried my NVT by changing tcouple=V-rescale i am getting the following error.. creating statusfile for 1 node... *ERROR: invalid enum 'V-rescale' for variable tcoupl, using 'No'* Ne

[gmx-users] regarding NVT

hello sir, i followed lysozyme tutorial to do dynamics for my protein.. but at the end of NVT equilibration, my temperature is at 243K.. but i set 300K to my mdp file .. mine is not getting equilibrium condition.. this is my nvt.mdp file title =GROMOS43a1 lipopeptide NVT equilibra

[gmx-users] regarding rmsd and md

hello sir, I performed dynamics for my lipopeptide... After md i thought of calculating rmsd... i did my md for 4ns.. when i plot graph for rmsd, i got plot til 2.2ns i dono why it came like this.. can anyone tell me why it is like this.. and also i like to clarify one doubt... If i do dynamic

[gmx-users] regarding NVT

hello sir, Thanks for your reply.. After NVT step i am getting 244K .. but i set temperature to 300K.. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before p

[gmx-users] regarding nvt

hello sir, sorry i left few lines while pasting my nvt.mdp input file thi is my nvt.mdp file title =GROMOS43a1 lipopeptide NVT equilibration define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md; leap-frog integrator nsteps

[gmx-users] regarding NVT equilibration

hello sir, i am following lysozyme tutorial for my dynamics. when i go for equilibration first we need to do NVT. there i set 300K ... At the end of NVT when i check my temperature using my edr file i am not getting equilbrium temp.. it showed 239K one time and sometime 329K like this..but not aro

[gmx-users] regarding top file

hello sir, i dono what i did was correct or not. But i did it. please tell me what i did was correct or not,, i tried two different ways to generate my top file. first i did prodrg for my whole lipopeptide and got its itp . pdb and gro file. then i included information about atomtype, bond, pairs

[gmx-users] regarding itp

hello sir, thanks for your reply.. sorry for disturbing you again and again.. i understood that i need to add my residue BFC in my rtp file and residuetype.dat file. i like to clarify one thing. i added BFC as lipid in my residuetypes.dat file. then i need to include my residue BFC in .rtp file. T

[gmx-users] regarding rtp file

hello sir, Thanks for your reply.. As you suggest i tried with all available forcefield for my lipopeptide but i am getting the same error,, *Processing chain 2 'A' (16 atoms, 1 residues) Warning: Starting residue BFC1 in chain not identified as Protein/RNA/DNA. Problem with chain definition, or

[gmx-users] regarding rtp file

hello sir, i go through the manual and your link.. i need to add BFC residue type in rtp file and residuetype.dat.. thing is i need to include charges angles bonds dihedrals impropers for residue in my rtp file ,, i dono how to define its value.. mine is 14 carbon fattyacid..(BFC) give some idea

[gmx-users] regarding topology

hello sir, Thanks for your reply. initially i tried with pdb2gmx command.but i got error. as i said mine is a cyclicheptapeptide. my fattyacid residue type is BFC. when i performed pdb2gmx -f protein.pdb -p protein.top -o protein.gro -ignh it showed error as *Processing chain 2 'A' (16 atoms,

[gmx-users] regarding rtp file

hello sir, Thanks for your reply.. i like to know is it better to do x2top for my whole protein instead of seperating fattyacid from aminoacid to generate rtp file and top file since mine is a cyclicheptapeptide.. so that i can use that top file for doing my energy minimization ,position restr ad

[gmx-users] regarding x2top

hello sir, thanks for your reply.. The thing is i seperated my fattyacid portion from aminoacid.. so carbon missing its bond. That 1st carbon linked to c, one double bonded o and glu aminoacid... how i need to model my input.. shall i need to draw my fattyacid portion alone in chemsketch and th

[gmx-users] regarding x2top error

hello sir, i tried to produce rtp file using x2top command for my file HETATM 123 C BFC A 1 0.446 -0.085 2.419 1.00 0.00 C HETATM 124 O BFC A 1 0.234 -0.665 3.482 1.00 0.00 O HETATM 125 CA BFC A 1 1.485 -0.637 1.467 1.00 0.00

[gmx-users] Test mail

Greetings, THis is a mail to test my gromacs mailing list connection -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscr