Re: [gmx-users] L-BFGS energy minimization not leading to wrapping of dna around cnt

Okay, thanks a lot. Majid From: Justin A. Lemkul To: Gromacs Users' List Sent: Wed, April 20, 2011 12:01:33 PM Subject: Re: [gmx-users] L-BFGS energy minimization not leading to wrapping of dna around cnt majid hasan wrote: > Okay, thanks. But t

Re: [gmx-users] L-BFGS energy minimization not leading to wrapping of dna around cnt

ast as you might need for very long simulations. -Justin Thanks again, Majid *From:* Justin A. Lemkul *To:* Discussion list for GROMACS users *Sent:* Wed, April 20, 2011 11:47:09 AM *Subject:* Re: [gmx-users] L-BFG

Re: [gmx-users] L-BFGS energy minimization not leading to wrapping of dna around cnt

from mdrun on laptop? Thanks again, Majid From: Justin A. Lemkul To: Discussion list for GROMACS users Sent: Wed, April 20, 2011 11:47:09 AM Subject: Re: [gmx-users] L-BFGS energy minimization not leading to wrapping of dna around cnt majid hasan wrote: &

Re: [gmx-users] L-BFGS energy minimization not leading to wrapping of dna around cnt

majid hasan wrote: Dear All, I tried to minimize the energy of CNT-DNA system in vacuum (just to make sure it works) using l-bfgs integrator. When I run in the .trr output file, ends of dna only move slightly towards cnt, but it doesn't wrap around it. Could anyone please guide me what can

[gmx-users] L-BFGS energy minimization not leading to wrapping of dna around cnt

Dear All, I tried to minimize the energy of CNT-DNA system in vacuum (just to make sure it works) using l-bfgs integrator. When I run in the .trr output file, ends of dna only move slightly towards cnt, but it doesn't wrap around it. Could anyone please guide me what can be the possible issues

Re: [gmx-users] l-bfgs

Thanks very much for you advises. Actually I just made one molecule of dppc using information from leterature about its bond lenghts and angles and so on... and then run md with that one molecule and then multipled it. First I made 16 dppc bilayer with 480 water and then from that 16dppc I made 32

Re: [gmx-users] l-bfgs

Hi Sona, Also look at the energies. If Erik's local energy minimum is indeed an all-time energy maximum (infinite energies, infinite forces), you're starting structure is indeed your worry. But then again, if you started from an energy minimized membrane, there's not much to minimize anymore. Now

Re: [gmx-users] l-bfgs

2 maj 2007 kl. 13.41 skrev Sona Aramyan: Hi everybody I'm trying to do em with l-bfgs integrator but it finishes with 0 steps. My system is 128dppc and 30 per lipid water. when I'm using steep integrator it converged to machine precision say 15 steps. What I'm suggesting is that my system has

[gmx-users] l-bfgs

Hi everybody I'm trying to do em with l-bfgs integrator but it finishes with 0 steps. My system is 128dppc and 30 per lipid water. when I'm using steep integrator it converged to machine precision say 15 steps. What I'm suggesting is that my system has very bad starting configuration and maybe it

Re: [gmx-users] L-BFGS energy minimization wrong!

zzhwise1 a écrit : > hi everyone ! >i have ask some questions about energy minimization before ,but > still,there are problems !this time it show: > --- > Program mdrun, VERSION 3.3.1

[gmx-users] L-BFGS energy minimization wrong!

hi everyone !    i have ask some questions about energy minimization before ,but still,there are problems !this time it show: --- Program mdrun, VERSION 3.3.1    Source code file: nsg