Re: [gmx-users] gen_vel during gradual NVT equilibration

2011-02-09 Thread Erik Marklund
Why don't you try simulated anealing instead? The you get a continous increase of the temprature over time. Erik bipin singh skrev 2011-02-09 12.27: Hi, I want to run NVT equilibration for a protein molecule and want to increase temperature gradually i.e. from 0 to 300 K over a 20 ps, but i

Re: [gmx-users] gen_vel during gradual NVT equilibration

2011-02-09 Thread Justin A. Lemkul
bipin singh wrote: Hi, I want to run NVT equilibration for a protein molecule and want to increase temperature gradually i.e. from 0 to 300 K over a 20 ps, but i have some doubts regarding this: 1)Whether I should read velocities from previous steps of NVT during gradual heating or every t

[gmx-users] gen_vel during gradual NVT equilibration

2011-02-09 Thread bipin singh
Hi, I want to run NVT equilibration for a protein molecule and want to increase temperature gradually i.e. from 0 to 300 K over a 20 ps, but i have some doubts regarding this: 1)Whether I should read velocities from previous steps of NVT during gradual heating or every time i have to generate vel

Re: [gmx-users] gen_vel

2010-05-15 Thread XAvier Periole
On May 15, 2010, at 10:22, shahab shariati wrote: Hi gromacs users I want to simulation of pr-dna as follows: 1) energy minimization 2) equilibration 3) full md. Should I use gen_vel=yes in mdp files for both (2) and (3) steps? In principle 3) should be the continuation of 2). So the an

[gmx-users] gen_vel

2010-05-15 Thread shahab shariati
Hi gromacs users I want to simulation of pr-dna as follows: 1) energy minimization 2) equilibration 3) full md. Should I use gen_vel=yes in mdp files for both (2) and (3) steps? Thank you so much for any help! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/

Re: [gmx-users] gen_vel error

2010-03-15 Thread Mark Abraham
On 16/03/2010 12:28 AM, Carla Jamous wrote: Hi everyone, Please I made an error during my simulation: I ran my simulation in the following way for many steps: grompp -v -f md.mdp -c ax.pdb -t bx.trr -e dx.edr -o ex.tpr -p fx.top mdrun -v -s ex.tpr -o gx.trr -c hx.pdb -x ix.xtc -e md.edr -g md.log

Re: [gmx-users] gen_vel error

2010-03-15 Thread Justin A. Lemkul
Carla Jamous wrote: Hi everyone, Please I made an error during my simulation: I ran my simulation in the following way for many steps: grompp -v -f md.mdp -c ax.pdb -t bx.trr -e dx.edr -o ex.tpr -p fx.top mdrun -v -s ex.tpr -o gx.trr -c hx.pdb -x ix.xtc -e md.edr -g md.log But in my em.mdp, I

[gmx-users] gen_vel error

2010-03-15 Thread Carla Jamous
Hi everyone, Please I made an error during my simulation: I ran my simulation in the following way for many steps: grompp -v -f md.mdp -c ax.pdb -t bx.trr -e dx.edr -o ex.tpr -p fx.top mdrun -v -s ex.tpr -o gx.trr -c hx.pdb -x ix.xtc -e md.edr -g md.log But in my em.mdp, I kept: gen_vel = yes So

Re: [gmx-users] gen_vel

2009-12-04 Thread Mark Abraham
leila karami wrote: Hi in which case in mdp file, gen_vel should be yes or no? ... when you want to generate velocities or not. See manual section 3.4, particularly 3.4.1 Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please sea

[gmx-users] gen_vel

2009-12-04 Thread leila karami
Hi in which case in mdp file, gen_vel should be yes or no? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use th

Re: [gmx-users] gen_vel

2007-03-27 Thread Mark Abraham
? wrote: HI EVERYBODY, I HAVE A PROBLEM WITH gen_vel.IF I MAKE AN ANALYZE WITH POSITION RESTRAINT I USED gen_vel=yes.AFTER FOR FULL MDP I USED gen_vel=no.AFTER THAT I USED gen_vel=no FOR AGAIN FULL.MDP.BUT I GOT VERY BAD RMSD GRAPHICS.ANY HELP ABOUT WHAT IS THE MEANING OF gen_vel=no,gen-vel=

Re: [gmx-users] gen_vel

2007-03-27 Thread Yang Ye
according to what you have described, it is correct. is your reference structure wrong for RMSD calculation? On 3/27/2007 8:56 PM, özge kül wrote: HI EVERYBODY, I HAVE A PROBLEM WITH gen_vel.IF I MAKE AN ANALYZE WITH POSITION RESTRAINT I USED gen_vel=yes.AFTER FOR FULL MDP I USED gen_vel=no

Re: [gmx-users] gen_vel

2007-03-27 Thread Tsjerk Wassenaar
GENERATE VELOCITIES FROM A maxwell DISTRIBUTION FOR ALL ATOMS OR NOT (keep from file or 0.0). SEE CHAPTER 7 OF THE gromacs MANUAL. YOUR WELCOME Tsjerk On 3/27/07, özge kül <[EMAIL PROTECTED]> wrote: HI EVERYBODY, I HAVE A PROBLEM WITH gen_vel.IF I MAKE AN ANALYZE WITH POSITION RESTRAINT I USE

[gmx-users] gen_vel

2007-03-27 Thread �zge
HI EVERYBODY, I HAVE A PROBLEM WITH gen_vel.IF I MAKE AN ANALYZE WITH POSITION RESTRAINT I USED gen_vel=yes.AFTER FOR FULL MDP I USED gen_vel=no.AFTER THAT I USED gen_vel=no FOR AGAIN FULL.MDP.BUT I GOT VERY BAD RMSD GRAPHICS.ANY HELP ABOUT WHAT IS THE MEANING OF gen_vel=no,gen-vel=yes?