Re: [gmx-users] deformation in simulation

; >> production > >> > > > file. > >> > > > > > >> > > > > > >> > > > > At first, run a restrained equilibrium. > >> > > > > > >> > > > > > >> > > > &g

Re: [gmx-users] deformation in simulation

t; > >> > > > > At first, run a restrained equilibrium. >> > > > > >> > > > > >> > > > > Then non-restrained equilibrium followed by production file. >> > > > > >> > > > >

Re: [gmx-users] deformation in simulation

t; > > > Then non-restrained equilibrium followed by production file. > > > > > > > > > > > > > > > Do not know the aim of your simulations. > > > > > > > > > > > > > > > Hope this answer helps. >

Re: [gmx-users] deformation in simulation

anks, > > > > > > > > Subashini.K > > > > > > > > > > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > > > > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of > RA

Re: [gmx-users] deformation in simulation

_ > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > > > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of RAHUL > > > SURESH <drrahulsur...@gmail.com> > > > Sent: Thursday, February 23, 2017 12:23 PM > > &g

Re: [gmx-users] deformation in simulation

ns. > > > > > > > > > Hope this answer helps. > > > > > > > > > Thanks, > > > > > > Subashini.K > > > > > > > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se

Re: [gmx-users] deformation in simulation

th.se < > > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of RAHUL > > SURESH <drrahulsur...@gmail.com> > > Sent: Thursday, February 23, 2017 12:23 PM > > To: gmx-us...@gromacs.org > > Subject: [gmx-users] deformation in simulation > >

Re: [gmx-users] deformation in simulation

-users-boun...@maillist.sys.kth.se> on behalf of RAHUL > > SURESH <drrahulsur...@gmail.com> > > Sent: Thursday, February 23, 2017 12:23 PM > > To: gmx-us...@gromacs.org > > Subject: [gmx-users] deformation in simulation > > > > Simulating a protein with 100re

Re: [gmx-users] deformation in simulation

_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of RAHUL > SURESH <drrahulsur...@gmail.com> > Sent: Thursday, February 23, 2017 12:23 PM > To: gmx-us...@gromacs.org > Subject: [gmx-users] deformation in simulation > > Simulat

Re: [gmx-users] deformation in simulation

> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of RAHUL > SURESH <drrahulsur...@gmail.com> > Sent: Thursday, February 23, 2017 12:23 PM > To: gmx-us...@gromacs.org > Subject: [gmx-users] deformation in simulation > > Simulating a protein with 100re

Re: [gmx-users] deformation in simulation

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of RAHUL SURESH <drrahulsur...@gmail.com> Sent: Thursday, February 23, 2017 12:23 PM To: gmx-us...@gromacs.org Subject: [gmx-users] deformation in simulation

Re: [gmx-users] deformation in simulation

I have generated my index file now using make_ndx command On Thu, Feb 23, 2017 at 1:18 PM, Amir Zeb wrote: > Hello, > > You would have xxx.xtc file. actually, this is your xtc file what ever the > name you have given, just put your corresponding xtc file therein. > Once you

Re: [gmx-users] deformation in simulation

Hello, You would have xxx.xtc file. actually, this is your xtc file what ever the name you have given, just put your corresponding xtc file therein. Once you are directed to prompt option, you should select 0 "system" On Wed, Feb 22, 2017 at 11:39 PM, RAHUL SURESH

Re: [gmx-users] deformation in simulation

Also I dont have traj.xtc file. On Thu, Feb 23, 2017 at 1:03 PM, RAHUL SURESH wrote: > what is that compact? > > And my protein is still within the system.(BOX) > > On Thu, Feb 23, 2017 at 12:40 PM, Amir Zeb wrote: > >> alright >> you first

Re: [gmx-users] deformation in simulation

what is that compact? And my protein is still within the system.(BOX) On Thu, Feb 23, 2017 at 12:40 PM, Amir Zeb wrote: > alright > you first centralize your system by the following command > trjconv -f traj.xtc -s md.tpr -n index.ndx -o md.xtc -pbc mol -ur compact > and

Re: [gmx-users] deformation in simulation

alright you first centralize your system by the following command trjconv -f traj.xtc -s md.tpr -n index.ndx -o md.xtc -pbc mol -ur compact and then visualize probably you would have solved it. This is some how visualization problem. On Wed, Feb 22, 2017 at 11:06 PM, RAHUL SURESH

Re: [gmx-users] deformation in simulation

using VMD On Thu, Feb 23, 2017 at 12:32 PM, Amir Zeb wrote: > how do you visualize your system structure? > > On Wed, Feb 22, 2017 at 10:58 PM, RAHUL SURESH > wrote: > > > Dear amir > > > > They are forming long bonds. I hope you understand what i

Re: [gmx-users] deformation in simulation

how do you visualize your system structure? On Wed, Feb 22, 2017 at 10:58 PM, RAHUL SURESH wrote: > Dear amir > > They are forming long bonds. I hope you understand what i mean. Like few > molecules move away from the protein still bonded. and they again converge > at

Re: [gmx-users] deformation in simulation

Dear amir They are forming long bonds. I hope you understand what i mean. Like few molecules move away from the protein still bonded. and they again converge at some point but again they do deform. On Thu, Feb 23, 2017 at 12:26 PM, Amir Zeb wrote: > Hey > I don't know

Re: [gmx-users] deformation in simulation

Hey I don't know very well about the problem you have. Did you minimize your system well converged? You may go for conjugate minimization All the best! On Wed, Feb 22, 2017 at 10:53 PM, RAHUL SURESH wrote: > Simulating a protein with 100residues for 200ns doesn't show

[gmx-users] deformation in simulation

Simulating a protein with 100residues for 200ns doesn't show any stability. There are some deformation(long-bonds) in the structure throughout the process. Why is that so? Can I choose any stable structure in between these 200ns, for example say 176ns. Or is there any other way to make them work