Dear gmxers,
According to my recent practice, we find that the Berensen methods for T-
and P- coupling can yield reasonable averaged density as a function of
temperature, but when the v-rescale method and the Parrinello-Rahman method are
employed for T- and P- coupling, somewhat unexpected re
Dear gmxers,
I have had tried to install gmx-4.5.4 by compiling the source code. The
first step ./configure finished without any error, but the second step running
make reported some errors as follows
/usr/lib64/gcc/x86_64-suse-linux/4.4/../../../../x86_64-suse-linux/bin/ld:
/usr/local/li
Dear gmxers,
I want to perform a constant-NPT MD simulation using gmx. By default, a,b,c
of 3D pbc box can change to compatile with the density. Whether can gmx change
a,b of 3D pbc box but unchange c? Please give me some hints. Thanks a lot.
Yours sincerely,
Chaofu Wu, Dr.--
gmx-users
Dear developers and users,
While I run grompp, one note is output: leapfrog does not yet support
Nose-Hoover chains, nhchainlength reset to 1. Note that I am using gmx-4.5.3,
and leapfrog for integration and Nose-Hoover for temperature coupling. I
remember that gmx-4.5.2 or below version does
Dear gmxers,
I am trying to calculate radial distribution function (RDF) between some
particles
and the radial axis of a SWNT. It is obvious tht the g_rdf can not calculate
it. How
to do this calculation? Are there such tools for doing it? Please kindly refer
it to me?
Thanks a lot for any
Dear gmxers,
I am planning to analyze order parameter using g_order, but some problems
always puzzle me. For convenience, I describe the first problem as follows:
Assume that there are two polymer chains H-[CH2-CH(OH)]n-H, now I want to
calculate the order parameter of two carbon atoms in t
, Dr.
-- 原始邮件 --
发件人: "Mark Abraham";
发送时间: 2010年11月29日(星期一) 晚上7:38
收件人: "Discussion list for GROMACS users";
主题: Re: [gmx-users] How to save the coordinates of all atoms inthe 2D-arrays
using xdrfile?
On 28/11/2010 12:12 AM,
Dear gmxers,
I am trying to perform an analysis on the trjectory file using xdrfile
library. First of all, I want to save the coordinates of all atoms in three
2D-arrays, i.e. xx[step-1][natom-1], yy[step-1][natom-1], zz[step-1][natom-1].
How to do so? Could you give me some hints, please? If
Dear gmxers,
I do not know whether this question is suitable here. If not, please just
neglect it. However, this question puzzles me greatly, that is, how to obtain
the coordinates of atom 100 with number in the frame 100 using xdrfile in C
code. Here 100 is only an example for some defined a
ist for GROMACS users";
主题: Re: [gmx-users] the first 10 missing interactions,except for exclusions...
add dihedral parameter for you EPON molecule.
Check this:
http://oldwww.gromacs.org/pipermail/gmx-users/2005-May/015044.html
2010/10/24 英雄不再寂寞
Dear gmxers,
I try t
--
发件人: "Justin A. Lemkul";
发送时间: 2010年10月24日(星期天) 上午8:20
收件人: "Discussion list for GROMACS users";
主题: Re: [gmx-users] the first 10 missing interactions,except for exclusions...
英雄不再寂寞 wrote:
> Dear gmxers,
> I try to simulate a complex syst
Dear gmxers,
I try to simulate a complex system using gmx-4.5.1. I have carried out the
minimization without any errors, but when it comes to molecular dynamics, some
errors are printed and given below. How to deal with this problem? Please give
me some hints. Thanks a lot for any reply.
ely, yours
Chaofu Wu, Dr.
-- 原始邮件 --
发件人: "Justin A. Lemkul";
发送时间: 2010年10月17日(星期天) 晚上8:21
收件人: "Discussion list for GROMACS users";
主题: Re: [gmx-users] A very strange problem about version of pdb2gmx
英雄不再寂寞 wrote:
> Dear gmxers,
>
Dear gmxers,
Yesterday, I posted a mail titled "pdb2gmx stop at "AtomType 1" " where I
mentioned that I used gmx-4.5.1. The resulting problem is again posted below.
Today, I turn to the gmx-4.0.7, and use the same pdb and rtp files with the
name modified to compatible to the version. Strangely
Date: Sat, 16 Oct 2010 08:36:00 -0400
From: "Justin A. Lemkul"
Subject: Re: [gmx-users] pdb2gmx stop at "AtomType 1"
To: Discussion list for GROMACS users
Message-ID: <4cb99c30.50...@vt.edu>
Content-Type: text/plain; charset=x-gbk; format=flowed
英雄不再寂寞 wrote:
> Dea
Dear gmx-users,
I have added the required residue groups in the rtp file. Then I run the
pdb2gmx using the following line for the top file, only to stop at " AtomType
1". No any message is given. I can not think out what is happening at all.
Please help me with this problem, thanks a lot. Not
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