Re: [gmx-users] Implicit solvent - Gromacs 4.5.4

2012-02-29 Thread Mark Abraham
On 29/02/2012 9:26 PM, Steven Neumann wrote: On Tue, Feb 28, 2012 at 10:50 PM, Justin A. Lemkul > wrote: Steven Neumann wrote: On Tue, Feb 28, 2012 at 6:33 PM, Justin A. Lemkul mailto:jalem...@vt.edu>

Re: [gmx-users] Implicit solvent - Gromacs 4.5.4

2012-02-29 Thread Steven Neumann
On Tue, Feb 28, 2012 at 10:50 PM, Justin A. Lemkul wrote: > > > Steven Neumann wrote: > > >> >> On Tue, Feb 28, 2012 at 6:33 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote: >> >> >> >>Steven Neumann wrote: >> >>I run energy minimization of my protein with implicit solvent: >>

Re: [gmx-users] Implicit solvent - Gromacs 4.5.4

2012-02-28 Thread Justin A. Lemkul
Steven Neumann wrote: On Tue, Feb 28, 2012 at 6:33 PM, Justin A. Lemkul > wrote: Steven Neumann wrote: I run energy minimization of my protein with implicit solvent: constraints = none integrator = steep dt

Re: [gmx-users] Implicit solvent - Gromacs 4.5.4

2012-02-28 Thread Mark Abraham
On 29/02/2012 1:11 AM, lina wrote: On Tue, Feb 28, 2012 at 10:07 PM, Steven Neumann wrote: Thank you Vedat! Why do you use -DFLEXIBLE in md and in em? Why dont you use constraint algorithm (LINCS) in your simulation? Otherwise, the system is easily explode with lots of LINCS warning. That

Re: [gmx-users] Implicit solvent - Gromacs 4.5.4

2012-02-28 Thread Steven Neumann
Thank you Vedat!!! On Tue, Feb 28, 2012 at 8:35 PM, vedat durmaz wrote: > ** > > hi jan/steven (?), > > you should know, in contrast to let's say justin lemkul, i haven't that > much experience with molecular simulations! > > actually, i don't expect large differences in conformational/statistic

Re: [gmx-users] Implicit solvent - Gromacs 4.5.4

2012-02-28 Thread Steven Neumann
On Tue, Feb 28, 2012 at 6:33 PM, Justin A. Lemkul wrote: > > > Steven Neumann wrote: > >> I run energy minimization of my protein with implicit solvent: >> >>constraints = none >> >>integrator = steep >> >>dt = 0.001 ; ps >> >>nsteps = 3 >> >>vdwtype = cut-off >> >>cou

Re: [gmx-users] Implicit solvent - Gromacs 4.5.4

2012-02-28 Thread vedat durmaz
hi jan/steven (?), you should know, in contrast to let's say justin lemkul, i haven't that much experience with molecular simulations! actually, i don't expect large differences in conformational/statistical properties depending on the usage of lincs constraints. usually i use them when sim

Re: [gmx-users] Implicit solvent - Gromacs 4.5.4

2012-02-28 Thread Justin A. Lemkul
Steven Neumann wrote: I run energy minimization of my protein with implicit solvent: constraints = none integrator = steep dt = 0.001 ; ps nsteps = 3 vdwtype = cut-off coulombtype = cut-off pbc = no nstlist = 0 ns_type = simple rlist = 0

Re: [gmx-users] Implicit solvent - Gromacs 4.5.4

2012-02-28 Thread Steven Neumann
I run energy minimization of my protein with implicit solvent: > constraints = none > > integrator = steep > > dt = 0.001 ; ps > > nsteps = 3 > > vdwtype = cut-off > > coulombtype = cut-off > > pbc = no > > nstlist = 0 > > ns_type = simple > > rlist = 0 ; this means all-vs-all (no cut-off),

Re: [gmx-users] Implicit solvent - Gromacs 4.5.4

2012-02-28 Thread Vedat Durmaz
thanks justin for clearing up these issues .. Am 28.02.2012 15:50, schrieb Justin A. Lemkul: Vedat Durmaz wrote: actually, as far as i know, the -DFLEXIBLE argument has no effect on simulations without explicit water ?! The #ifdef FLEXIBLE block does only affect explicit water, unless

Re: [gmx-users] Implicit solvent - Gromacs 4.5.4

2012-02-28 Thread Justin A. Lemkul
Vedat Durmaz wrote: actually, as far as i know, the -DFLEXIBLE argument has no effect on simulations without explicit water ?! The #ifdef FLEXIBLE block does only affect explicit water, unless the topology is somehow modified to use this type of term (probably not). It shouldn't be use

Re: [gmx-users] Implicit solvent - Gromacs 4.5.4

2012-02-28 Thread Vedat Durmaz
actually, as far as i know, the -DFLEXIBLE argument has no effect on simulations without explicit water ?! i just copied the "define" line from my explicit simulation systems .. so, the only define value, that has a meaning is -DPOSRESHELIX. i didn't use constraints for the first time in my l

Re: [gmx-users] Implicit solvent - Gromacs 4.5.4

2012-02-28 Thread Steven Neumann
Thank you all! How about -DFLEXIBLE in both em and md? Steven On Tue, Feb 28, 2012 at 2:13 PM, Justin A. Lemkul wrote: > > > lina wrote: > >> On Tue, Feb 28, 2012 at 10:07 PM, Steven Neumann >> wrote: >> >>> Thank you Vedat! >>> >>> Why do you use -DFLEXIBLE in md and in em? >>> Why dont you

Re: [gmx-users] Implicit solvent - Gromacs 4.5.4

2012-02-28 Thread Justin A. Lemkul
lina wrote: On Tue, Feb 28, 2012 at 10:07 PM, Steven Neumann wrote: Thank you Vedat! Why do you use -DFLEXIBLE in md and in em? Why dont you use constraint algorithm (LINCS) in your simulation? Otherwise, the system is easily explode with lots of LINCS warning. A system that is unstable

Re: [gmx-users] Implicit solvent - Gromacs 4.5.4

2012-02-28 Thread lina
On Tue, Feb 28, 2012 at 10:07 PM, Steven Neumann wrote: > Thank you Vedat! > > Why do you use -DFLEXIBLE in md and in em? > Why dont you use constraint algorithm (LINCS) in your simulation? Otherwise, the system is easily explode with lots of LINCS warning. Also thanks Vedat for sharing, Best r

Re: [gmx-users] Implicit solvent - Gromacs 4.5.4

2012-02-28 Thread Steven Neumann
Thank you Vedat! Why do you use -DFLEXIBLE in md and in em? Why dont you use constraint algorithm (LINCS) in your simulation? Steven On Tue, Feb 28, 2012 at 12:14 PM, Vedat Durmaz wrote: > > hi steven, > > i've been simulating a 33 AA peptide for the past two days using implicent > solvent in

Re: [gmx-users] Implicit solvent - Gromacs 4.5.4

2012-02-28 Thread Vedat Durmaz
hi steven, i've been simulating a 33 AA peptide for the past two days using implicent solvent in order to achieve a proper folding. i haven't added counterions, however, the systems shows nice results according to what i've expected. the mdrun command (for the extension) for our hardware lo