Dear Emanuel,
Thank you so much for the response.
I did the H bond count using the g_hbond. After this these H bond are
correlated against time right?? I just want to make sure I got it right. And
more over I should give a distance constrain so as to give me the existence of
water at a time.
Yao Yao wrote:
Hi all,
I am constructing a new molecule in OPLS force field. Though I modified
ffbonded.itp, ffnonbonded.itp, atomtypes.atp
aminoacids.rtp, it still gives error "Unknown Molecule_Atomtype". I have
opened all the files in the OPLS force field but really do not see any
other f
Hi there,
I am also doing FEP calculations and I am also using sd as integrator. The
problem that I am having with this integrator is the temperature coupling
(NTP). I am setting the targeted temperature of the system on 300K, for 2
Groups, Protein_and_ligand and Solvent. g_energy gives me 303
Try running for longer and look at the convergence of the temperatures
over time. I suspect that what you are reporting is actually just
statistical noise.
I am not sure about using the sd integrator and defining multiple
temperature coupling groups... If you define the same temperature for
C Colenso wrote:
Hi Justin,
I got your email from the Gromacs mailing list...I hope you don't mind.
I have a problem with pdb2gmx.
I have downloaded the 4.5.4 version of gromacs, no luck, I have consulted
the mailing lists and bugzillas, and tried every suggestion but this is
still not fixin
Thanks for your important advice, I am extending my simulation to 60ns, if it
is still not long enough, I’ll extend another time. Thank you.
发件人: Jianguo Li [mailto:ljg...@yahoo.com.sg]
发送时间: 2011年8月22日 9:52
收件人: KONG Xian
主题: Re: Re:the mdp parameters for localpressure calculation using
Hi
what do I need for a md with gromacs? I made a tutorial in which I download an
example file, but what I I don't have such a file downloaded from the pdb?
What do I need to create a first input file?
Greetings
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mai
Joschua Sterzenbach wrote:
Hi
what do I need for a md with gromacs? I made a tutorial in which I
download an example file, but what I I don't have such a file downloaded
from the pdb?
What do I need to create a first input file?
To run a simulation, you need coordinates (.gro,.pdb, etc)
Hello,
I have xpm matrix file, for converting this file to ps format I am using xpm2ps
e.g: xpm2ps -f file.xpm -o file.eps . But there is no axis range label
mentioned for x and y-axis,
in ps file.Please let me know how to set x and y axis range label in ps file.
for example I want to set the x an
bipin singh wrote:
Hello,
I have xpm matrix file, for converting this file to ps format I am using xpm2ps
e.g: xpm2ps -f file.xpm -o file.eps . But there is no axis range label
mentioned for x and y-axis,
in ps file.Please let me know how to set x and y axis range label in ps file.
for example
Yao Yao wrote:
Hi Justin,
Thanks for your reply. Here is the exact error message,
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
checking input for internal consistency...
processing topology...
Opening library file /s
Dear gmx-users,
I have posted this question on gmx-users list few days ago 2-3 times.
But I didn't receive any suggestion/reply.
I have searched a lot on previous posts related to Viscosity calculations
but unable to
get any suitable reply.
Please reply if someone has solution of following problem
Hello,
I am using the below .m2p file as input for xpm2ps, but not able to
get axis range label.
; Matrix options
titlefont = Helvetica ; Matrix title Postscript Font name
titlefontsize = 20.0 ; Matrix title Font size (pt)
legend = yes ; Show the legend
lege
Hi all,
I am using Gromacs 4.0.5 with the forcefield amber03 in a red hat linux machine to simulate a protein-DNA complex. Eventhough I manually edited my pdb file to adhere to the amber nomenclature, I get the below error.
I have not been able to pinpoint where in the pdb file, ffamber03
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