omacs.org>
Sent: Thursday, September 7, 2017 3:02:10 PM
Subject: Re: [gmx-users] DPOSRES not working
On 9/7/17 8:52 AM, Sergio Manzetti wrote:
> Hey Justin , you sound like Mark Zuckerberg :)
I don't know whether that's good or bad...
> Here is the command I used:
>
> gm
] | [ http://www.phap.no/ | FAP ]
From: "Justin Lemkul" <jalem...@vt.edu>
To: "gmx-users" <gmx-us...@gromacs.org>
Sent: Thursday, September 7, 2017 2:55:05 PM
Subject: Re: [gmx-users] DPOSRES not working
On 9/7/17 8:45 AM, Sergio Manzetti wrote:
It seems that GMX sim
/ | Nanofactory
] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ | FAP ]
From: "Justin Lemkul" <jalem...@vt.edu>
To: "gmx-users" <gmx-us...@gromacs.org>
Sent: Thursday, September 7, 2017 2:55:05 PM
Subject: Re: [gmx-users] DPOSRES not working
On
ot; <jalem...@vt.edu>
To: "gmx-users" <gmx-us...@gromacs.org>
Sent: Thursday, September 7, 2017 2:28:23 PM
Subject: Re: [gmx-users] DPOSRES not working
On 9/7/17 5:28 AM, Sergio Manzetti wrote:
Hi Johannes, yes, they are there in both cases:
; Include Position restraint file
#
://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ | FAP ]
From: "Justin Lemkul" <jalem...@vt.edu>
To: "gmx-users" <gmx-us...@gromacs.org>
Sent: Thursday, September 7, 2017 2:28:23 PM
Subject: Re: [gmx-users] DPOSRES not working
On 9/7/17 5:28 AM, Sergio Man
On 9/7/17 5:28 AM, Sergio Manzetti wrote:
Hi Johannes, yes, they are there in both cases:
; Include Position restraint file
#ifdef POSRES
#include "posre_DNA_chain_E.itp"
#endif
Do you have a position restraint energy term written in your .log file,
and if so, what is its magnitude? Does
;
To: "gmx-users" <gmx-us...@gromacs.org>
Sent: Thursday, September 7, 2017 11:29:03 AM
Subject: Re: [gmx-users] DPOSRES not working
Okay, but what did you define in your topologies for your DNA chains:
#include "topol_DNA_chain_E.itp"
#include "topol_DNA_ch
Johannes" <j.herm...@lrz.tu-muenchen.de>
To: "gmx-users" <gmx-us...@gromacs.org>
Sent: Thursday, September 7, 2017 11:18:29 AM
Subject: Re: [gmx-users] DPOSRES not working
Dear Sergio,
how did you define the position restrain in your topology? Check your
topolog
To: "gmx-users" <gmx-us...@gromacs.org>
Sent: Thursday, September 7, 2017 11:18:29 AM
Subject: Re: [gmx-users] DPOSRES not working
Dear Sergio,
how did you define the position restrain in your topology? Check your
topology and position restrain file.
All the best
Dear Sergio,
how did you define the position restrain in your topology? Check your
topology and position restrain file.
All the best
Johannes
On 07.09.2017 11:07, Sergio Manzetti wrote:
Hello, I am running 5 simulations with the given mdp:
title = DNA in water stabilization
cpp =
Hello, I am running 5 simulations with the given mdp:
title = DNA in water stabilization
cpp = /lib/cpp
include = -I../top
define = -DPOSRES
integrator = md
dt = 0.002
nsteps = 1000
nstxout = 5000
nstvout = 5000
nstlog = 5000
nstenergy = 300
nstxout-compressed = 300
11 matches
Mail list logo
