On 07/07/2013 03:18 AM, Justin Lemkul wrote:
This problem can be solved by remembering to complete step 5 of
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field.
As Mark notes, though, this issue is entirely separate from your
initial problem.
-Justin
Hello
hi
must all mdp files be similar for g_lie program? shouldn't i use of PME in all
mdp files?
what edr file must i use as input file for g_lie?
many thanks
/
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On 07/06/2013 10:17 PM, Mark Abraham wrote:
That's a completely different output. I think both your executables
are broken, somehow. Clean the build and install trees and try again
:-)
Mark
Hello Mark:
thanks a lot for kind messages. The previous problem was solved by
Justin's
The error happens on the last line it reached. Take a look at it :-)
Mark
On Sun, Jul 7, 2013 at 9:52 AM, Albert mailmd2...@gmail.com wrote:
On 07/06/2013 10:17 PM, Mark Abraham wrote:
That's a completely different output. I think both your executables
are broken, somehow. Clean the build
And please replicate it with a more recent 4.5.x or 4.6.x first!
Mark
On Sun, Jul 7, 2013 at 3:17 AM, Justin Lemkul jalem...@vt.edu wrote:
On 7/6/13 8:21 AM, rama david wrote:
Hi Friends,
I am working on peptide self assembly.
I simulated two peptide which are random coil and apart
On 07/07/2013 10:23 AM, Mark Abraham wrote:
Program grompp, VERSION 4.6.3
Source code file:
kernel/topdirs.c, line: 106
Hello Mark:
thanks a lot for kind reply. Do you mean the above information? I open
this file and here is the line 106:
gmx_fatal(FARGS, Invalid angle type %d, type);
Dear all,
I am planing to do pulling on a bundle of elongated proteins. I compared
two box types - triclinic and
dodecahedron. The volume and total number of atoms (protein+solvent),
following the editconf and genbox commands,
were 522.06 nm3 and 47921 for triclinic box and 2444.19 nm3 and 24
Dear gmx users,
I' d like to get pdb files from trajectory, then used the trjconv,
# trjconv -f trajout.xtc -o out.pdb -sep
It gives fatal error as this:
Can not open file:
topol.tpr
Sincerely,
Shima
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Hi Shima,
You need to give a reference structure with the -s option. Otherwise the
program assumes you mean to use topol.tpr, which isn't present.
Cheers,
Tsjerk
On Sun, Jul 7, 2013 at 11:51 AM, Shima Arasteh
shima_arasteh2...@yahoo.comwrote:
Dear gmx users,
I' d like to get pdb files
Dear Shima
What is the name of your .tpr file?
If you had not chosen any name for it, Gromacs will generate a
topol.tpr for you and in my idea this error will not occur,
if not, you have to mention your file (e.g. Filename.tpr) explicitely
in your command line!
I hope this help you
Best
On Sun,
On 07/07/2013 10:23 AM, Mark Abraham wrote:
The error happens on the last line it reached. Take a look at it:-)
Mark
Hi Mark:
thanks again for kind helps these days. My problem solved now: my
original charmm file was mixed with old parameters which I worked on
before. After I start from
Hi Cyrus,
In a rectangular box (which is a specific case of a triclinic box) your
molecule can't rotate freely without significant chance to run into its
periodic image, invalidating whatever result you get. So, unless rotation
is of no concern, or can be cirrcumvented, you'll need to use a
hi
please help me
must all mdp files to be similar for g_lie program? shouldn't i use of PME in
all mdp files?
what edr file must i use as input file for g_lie?
best regards
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Dear all and Tsjerk Wassenar,
I could not grasp how a rectangular box will be a problem. Lets assume a I
have a cylinder of radius r (nm) and height h (nm) with hr. I place the
cylinder aligned along z-axis and then in a rectangular box with dimension
2r+2.0 nm, 2r+2.0 nm and 2h+2.0 nm. My
On Sun, Jul 7, 2013 at 4:15 PM, akcyrus akcy...@gmail.com wrote:
Dear all and Tsjerk Wassenar,
I could not grasp how a rectangular box will be a problem. Lets assume a I
have a cylinder of radius r (nm) and height h (nm) with hr. I place the
cylinder aligned along z-axis and then in a
Dear all,
The only tutorial on umbrella sampling by Justin (
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html)
assumes a rectangular box and pulling is done to separate chains. Is it
true that the approach worked solely because one of the reference chains
On 7/7/13 11:00 AM, akcyrus wrote:
Dear all,
The only tutorial on umbrella sampling by Justin (
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html)
assumes a rectangular box and pulling is done to separate chains. Is it
true that the approach worked
Dear gmx users,
I have a 10 ns simulation trajectory, and like to get some particular frames of
it. In fact I want to find the frames in which a specified coordinate is filled
with a water molecule, and then pick that frame as an initial structure for the
next steps.
Is there any script
On 7/7/13 1:14 PM, Shima Arasteh wrote:
Dear gmx users,
I have a 10 ns simulation trajectory, and like to get some particular frames of
it. In fact I want to find the frames in which a specified coordinate is filled
with a water molecule, and then pick that frame as an initial structure for
Dear Sir,
Thanks so much..
now what's the solution? Should I increase the box size?
Already I have centered the protein and fixed the POPE membrane size.
Can you tell me how to increase the box size? or is there any other
solution?
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Thankyou!! sir. Your answer helped a lot.
Richa
On 2 July 2013 13:04, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hi Richa,
From your explanation, I understand you want to know the sum of distances
between each frame and its corresponding filtered frame. I think it makes
more sense to sum
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