Re: [gmx-users] Inconsistent results in different clusters and cores

2013-05-17 Thread tarak karmakar
oop for jaanus.k...@eesti.ee >> >> Tarak >> >> >> -- Forwarded message ------ >> From: tarak karmakar >> To: Discussion list for GROMACS users >> Cc: >> Date: Fri, 17 May 2013 15:50:25 +0530 >> Subject: Re: [gmx-users] I

Re: [gmx-users] Inconsistent results in different clusters and cores

2013-05-17 Thread tarak karmakar
; Status: 5.0.0 > Diagnostic-Code: X-Postfix; mail forwarding loop for jaanus.k...@eesti.ee > > Tarak > > > -- Forwarded message -- > From: tarak karmakar > To: Discussion list for GROMACS users > Cc: > Date: Fri, 17 May 2013 15:50:25 +0530 > Subject:

Re: [gmx-users] Inconsistent results in different clusters and cores

2013-05-17 Thread tarak karmakar
...@eesti.ee Tarak -- Forwarded message -- From: tarak karmakar To: Discussion list for GROMACS users Cc: Date: Fri, 17 May 2013 15:50:25 +0530 Subject: Re: [gmx-users] Inconsistent results in different clusters and cores On Fri, May 17, 2013 at 5:36 PM, Mark Abraham wrote: >

Re: [gmx-users] Inconsistent results in different clusters and cores

2013-05-17 Thread Mark Abraham
On Fri, May 17, 2013 at 1:23 PM, Justin Lemkul wrote: > > > On 5/17/13 6:20 AM, tarak karmakar wrote: > >> I have read the 'implementation of charmm in gromacs' by bjelkmar, >> JCTC. There they have used following cut-offs >> coulombtype=PME >> rcoulomb=1.2 >> vdwtype=switch >> rvdw=1.2 >> rvdw-s

Re: [gmx-users] Inconsistent results in different clusters and cores

2013-05-17 Thread Justin Lemkul
On 5/17/13 6:20 AM, tarak karmakar wrote: I have read the 'implementation of charmm in gromacs' by bjelkmar, JCTC. There they have used following cut-offs coulombtype=PME rcoulomb=1.2 vdwtype=switch rvdw=1.2 rvdw-switch=1.0 I am not sure about rlist. It's really unnecessary to spam the list

Re: [gmx-users] Inconsistent results in different clusters and cores

2013-05-17 Thread tarak karmakar
I have read the 'implementation of charmm in gromacs' by bjelkmar, JCTC. There they have used following cut-offs coulombtype=PME rcoulomb=1.2 vdwtype=switch rvdw=1.2 rvdw-switch=1.0 I am not sure about rlist. Regards, Tarak On Fri, May 17, 2013 at 1:46 PM, tarak karmakar wrote: > Now if I incr

Re: [gmx-users] Inconsistent results in different clusters and cores

2013-05-17 Thread tarak karmakar
Now if I increase the rlist it is showing that With coulombtype = PME, rcoulomb must be equal to rlist If you want optimal energy conservation or exact integration use PME-Switch I don't know exactly what will be the best set up with charmm force field. Any suggestion please!! Thanks, Tara

Re: [gmx-users] Inconsistent results in different clusters and cores

2013-05-17 Thread tarak karmakar
What about Dispersion Correction ? But if I use this set of informations ; 7.3.3 Run Control integrator = md; md integrator tinit = 0 ; [ps] starting time for run dt = 0.001 ; [ps] time step

Re: [gmx-users] Inconsistent results in different clusters and cores

2013-05-12 Thread tarak karmakar
Oh ! Thanks a lot Justin. I'll rerun all my jobs with this corrected mdp. Restrains things I didn't follow properly, anyway I'll read about this. On Sun, May 12, 2013 at 11:27 PM, Justin Lemkul wrote: > > > On 5/12/13 1:53 PM, tarak karmakar wrote: > >> Thanks, >> >> I have used CGENFF force fi

Re: [gmx-users] Inconsistent results in different clusters and cores

2013-05-12 Thread Justin Lemkul
On 5/12/13 1:53 PM, tarak karmakar wrote: Thanks, I have used CGENFF force field parameters for the ligand generated from PARMCHEM with 0 penalties. For protein I have used CHARMM36 force field. my npt.mdp file is as follows, ; 7.3.3 Run Control integrator = md Bug 1021 was onl

Re: [gmx-users] Inconsistent results in different clusters and cores

2013-05-12 Thread tarak karmakar
Thanks, I have used CGENFF force field parameters for the ligand generated from PARMCHEM with 0 penalties. For protein I have used CHARMM36 force field. my npt.mdp file is as follows, ; 7.3.3 Run Control integrator = md tinit = 0 dt = 0.001 nste

Re: [gmx-users] Inconsistent results in different clusters and cores

2013-05-12 Thread Justin Lemkul
On 5/12/13 1:34 PM, tarak karmakar wrote: Thanks Justin for the Quick and Helpful reply. Yes. If I am right, the chaotic behavior of the simulations is inherent and can be assessed statistically by generating several independent trajectories and analyzing their similar outcomes. But with t

Re: [gmx-users] Inconsistent results in different clusters and cores

2013-05-12 Thread tarak karmakar
Thanks Justin for the Quick and Helpful reply. Yes. If I am right, the chaotic behavior of the simulations is inherent and can be assessed statistically by generating several independent trajectories and analyzing their similar outcomes. But with the same '.mdp' file I am getting TOO much diffe

Re: [gmx-users] Inconsistent results in different clusters and cores

2013-05-12 Thread Justin Lemkul
On 5/12/13 1:17 PM, tarak karmakar wrote: Dear All, I am simulating a protein in water to check the ligand movement over a time span. I haveminimized the system in STEEP and CG and after that heated from 0K - 300K within a time span of 300 ps. Then, I performed the NPT production run

[gmx-users] Inconsistent results in different clusters and cores

2013-05-12 Thread tarak karmakar
Dear All, I am simulating a protein in water to check the ligand movement over a time span. I haveminimized the system in STEEP and CG and after that heated from 0K - 300K within a time span of 300 ps. Then, I performed the NPT production runs. In two clusters I have got different results