Re: Fwd: [gmx-users] SD integrator

2013-09-15 Thread Dr. Vitaly Chaban
13 1:43 PM, "Dr. Vitaly Chaban" >> wrote: >> >> >> >>> There must be some problem with degrees of freedom in your system... >> >>> >> >>> >> >>> Dr. Vitaly V. Chaban >> >>> >> >>>

Re: Fwd: [gmx-users] SD integrator

2013-09-15 Thread HANNIBAL LECTER
am position restraining the CNT group. That affects the degrees of > >> freedom. > >> On Sep 13, 2013 1:43 PM, "Dr. Vitaly Chaban" > wrote: > >> > >>> There must be some problem with degrees of freedom in your system... > >>> >

Re: Fwd: [gmx-users] SD integrator

2013-09-13 Thread Dr. Vitaly Chaban
te: >> >>> There must be some problem with degrees of freedom in your system... >>> >>> >>> Dr. Vitaly V. Chaban >>> >>> >>> ------ Forwarded message -- >>> From: HANNIBAL LECTER >>> Date: Fri, Sep 1

Fwd: [gmx-users] SD integrator

2013-09-13 Thread Dr. Vitaly Chaban
There must be some problem with degrees of freedom in your system... Dr. Vitaly V. Chaban -- Forwarded message -- From: HANNIBAL LECTER Date: Fri, Sep 13, 2013 at 7:15 PM Subject: [gmx-users] SD integrator To: Discussion list for GROMACS users Hi all, I have been posting

[gmx-users] SD integrator

2013-09-13 Thread HANNIBAL LECTER
Hi all, I have been posting for a while with my problems in simulating peptides inside CNTs. After a lot of trials it seems like simulating the CNT with bonds and angles seems like a wise thing to do. I am using the SD integrator + PR barostat. It seems like improper thermostatting can blow up th

Re: [gmx-users] sd integrator

2011-09-21 Thread Mark Abraham
On 22/09/2011 9:57 AM, Sai Pooja wrote: But is the effect of varying ld_seed.. can that make different trajectories stochastic? Any single MD or SD trajectory is literally stochastic. Either can start from the same point with respectively different ld_seed or gen_seed and diverge. Mark O

Re: [gmx-users] sd integrator

2011-09-21 Thread Sai Pooja
But is the effect of varying ld_seed.. can that make different trajectories stochastic? On Wed, Sep 21, 2011 at 7:40 PM, Mark Abraham wrote: > On 22/09/2011 6:21 AM, Sai Pooja wrote: >> >> Hi, >> >> The sd integrator is described in the manual as follows: >> sd >> An accurate leap-frog stochast

Re: [gmx-users] sd integrator

2011-09-21 Thread Mark Abraham
On 22/09/2011 6:21 AM, Sai Pooja wrote: Hi, The sd integrator is described in the manual as follows: sd An accurate leap-frog stochastic dynamics integrator. Four Gaussian random number are required per integration step per degree of freedom. With constraints, coordinates needs to be constrained

[gmx-users] sd integrator

2011-09-21 Thread Sai Pooja
Hi, The sd integrator is described in the manual as follows: sd An accurate leap-frog stochastic dynamics integrator. Four Gaussian random number are required per integration step per degree of freedom. With constraints, coordinates needs to be constrained twice per integration step. Depending on