Dear GMX-users,
In the old website, I was able to search any topics (questions or answers) by
simply typing key words. But, it looks like, in the new website, I need to
open each archives for each year and month. Is there any way that I can search
more easily? Would you please tell me h
* Vitaly V. Chaban [2009-06-26 23:31:38 +0300]:
Hi,
In what units C6 constants are present in the force field files?
Hm [ C6/r^6 ] should yield an energy unit, so perhaps kJ * nm^6 / mol ??
However the C6 constants in the force field fields correspond to
different parameters of the LJ po
What are the exact functional forms for the three dihedral type functions
(listed on page 90 of the GROMACS Manual). I might have them figured out, but
I can't find anything that confirms that I do.
_
MSN 메신저의 차세대 버전, Windows Live
Hi,
In what units C6 constants are present in the force field files?
Thank you,
Vitaly
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PERFECT!!
Thanks Tsjerk!!
Best wishes!!
2009/6/26 Tsjerk Wassenaar
> Hi Guilherme,
>
> These parameters are kept in the later series 53a5 and 53a6.
>
> Cheers,
>
> Tsjerk
>
> On Fri, Jun 26, 2009 at 7:19 PM, Guilherme Menegon
> Giesel wrote:
> > Hello folks!!!
> >
> > I'm trying make simulation
Dave Hassan wrote:
Hi,
I'm trying to run a simple simulation of a DNA hairpin pdb entry 1pqt.
When I run pdb2gmx with the G43a1 force field I get the error:
Warning: 'DG' not found in residue topology database, trying to use 'DGUA'
---
Pro
Hi,
I'm trying to run a simple simulation of a DNA hairpin pdb entry 1pqt.
When I run pdb2gmx with the G43a1 force field I get the error:
Warning: 'DG' not found in residue topology database, trying to use 'DGUA'
---
Program pdb2gmx, VERSION 4
Hi Guilherme,
These parameters are kept in the later series 53a5 and 53a6.
Cheers,
Tsjerk
On Fri, Jun 26, 2009 at 7:19 PM, Guilherme Menegon
Giesel wrote:
> Hello folks!!!
>
> I'm trying make simulations with nucleic acids with GROMOS. I know that was
> published the article " An improved nucle
Independently of your ATP position, your system may explode or show
LINCS warnings if you use pressure and temperature coupling. I had these
problem, and corrected it removing the pressure coupling. Pressure
coupling will let your system expand in response to the heat, and if the
positions are
Hello folks!!!
I'm trying make simulations with nucleic acids with GROMOS. I know that was
published the article " An improved nucleic acid parameter set for the
GROMOS force field", showing new parameters to describe nucleic acids
conformations. Such parameters was inserted in a new force field:
Dear GROMACs users,
we have a task to use Amber force fields for protein-ligand complexes for
GROMACS MD simulation.
Which strategy is better to use?
1. To make .inpcrd and .prmtop files and then apply amb2gmx.pl script. Is
output for the protein-ligand complex for this script will be correct?
Hi GMXers,
according to the man page of g_dist, the -n option is optional. But when
I try to use g_dist without -n (and without an index.ndx in the working
directory), I get the following error:
---
Program g_dist, VERSION 4.0.5
Source code file
This is neat! Thanks
http://code.google.com/p/acpypi/wiki/TutorialAcpypi4Gromacs
On Fri, Jun 26, 2009 at 9:36 AM, Alan wrote:
> Hi there,
> How about taking a look at acpypi.googlecode.com and its wikis?
> I hope it can help you.
> Alan
> On Fri, Jun 26, 2009 at 14:27, wrote:
>>
>> Hello,
>>
>> I
Hi there,
How about taking a look at acpypi.googlecode.com and its wikis?
I hope it can help you.
Alan
On Fri, Jun 26, 2009 at 14:27, wrote:
>
> Hello,
>
> I'm trying to figure out how I can merge the ligand and receptor
> files. I used this script to prep a ligand I treated with GAFF
>
> perl
Jack Shultz wrote:
Hello,
I'm trying to figure out how I can merge the ligand and receptor
files. I used this script to prep a ligand I treated with GAFF
perl amb2gmx.pl --prmtop test1.prmtop --crd test1.inpcrd --outname ligand
This results in ligand.top & ligand.gro
Then I prepped a recept
Hello,
I'm trying to figure out how I can merge the ligand and receptor
files. I used this script to prep a ligand I treated with GAFF
perl amb2gmx.pl --prmtop test1.prmtop --crd test1.inpcrd --outname ligand
This results in ligand.top & ligand.gro
Then I prepped a receptor
pdb2gmx_d -f fzd2.p
Jérôme Baffreau wrote:
Thanks for your answer.
Actually no my run did not finish normally the first time (it has
been stopped after 7 days because of the time limitation on the
cluster it was running on). So I started it again (I ran the same
command and added the option "-append yes") and
wuxiao wrote:
> Dear gmx users, While I am running grompp, many errors are identified as
> follows: Error 124 [file **.top, line ] No default Ryckaert-Bell types
> What happened to this? How to cope with this problem?
You have specified an R-B dihedral for which no parameters exist. You'll
Dear gmx users,
While I am running grompp, many errors are identified as follows:
Error 124 [file **.top, line ]
No default Ryckaert-Bell types
What happened to this? How to cope with this problem?
Any reply would be acknowledged very much.
Sincerely
Chaofu Wu
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