Could someone please tell me what exactly is printed in the pullf.xvg
file from an umbrella sampling simulation?
Is it the total force acting the COM of the pull group - i.e. force from
regular potential plus the umbrella force or just the unbiased force?
Krzysztof Kuczera
--
Krzysztof
to sample the folded state. Another
reason might be having experimental data at lower T, but this
is problematic, as it is hard to model temperature-dependent properties
with simple force fields.
Krzysztof Kuczera
On 4/27/12 10:06 AM, Tomek Wlodarski wrote:
Hi Mark,
Thanks for reply.
The problem
atom names
in the lipids
Krzysztof Kuczera
On 4/15/12 12:09 PM, Tomek Wlodarski wrote:
Hi,
I would like to simulate protein in DMPC bilayer in Charmm36 ff.
I checked mailing list and KALP-15 tutorial, but still I have a few
basic questions.
1) I have problem with DMPC bilayer...
- VMD membrane
You probably need to save velocities at least every 10 fs;
look at your plot on a fine enough time scale - say 0-1 ps range
probably running in NVE ensemble would help as well
Krzysztof Kuczera
On 3/29/12 10:42 AM, Ignacio Fernández Galván wrote:
Dear all,
I'm trying to estimate
( the 100 ns solvated bilayer
simulation is already on my list)
Greetings
Krzysztof Kuczera
--
Krzysztof Kuczera
Departments of Chemistry and Molecular Biosciences
The University of Kansas
2010 Malott Hall
Lawrence, KS 66045
Tel: 785-864-5060 Fax: 785-864-5396 email: kkucz...@ku.edu
http
are found.
It would be very helpful if I could find the parameters of ACE and NME
caps for the charmm27 force field and the parameters of NME for
gromos43a1 and gromos53a6, in order to integrate them in the parameter
files of Gromacs.
Thanks in advance
--
Krzysztof Kuczera
Professor
,
--
Krzysztof Kuczera
Professor
Departments of Chemistry and Molecular Biosciences
The University of Kansas
2010 Malott Hall
Lawrence, KS 66045
Tel: 785-864-5060 Fax: 785-864-5396 email: kkucz...@ku.edu
http://oolung.chem.ku.edu/~kuczera/home.html
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gmx-users mailing listgmx-users@gromacs.org
http
. 4.5.4 and lower
don't have
ACE in charmm27.
On 2012-01-06 12 tel:2012-01-06%2012:59:56PM -0600,
Krzysztof Kuczera wrote:
Here is the blocking group from
gromacs-4.5.5/share/top/charmm27.ff/aminoacids.rtp
KK
[ ACE
post? Read http://www.gromacs.org/Support/Mailing_Lists
--
Krzysztof Kuczera
Professor
Departments of Chemistry and Molecular Biosciences
The University of Kansas
2010 Malott Hall
Lawrence, KS 66045
Tel: 785-864-5060 Fax: 785-864-5396 email: kkucz...@ku.edu
http://oolung.chem.ku.edu/~kuczera
)?
Thanks.
--
Krzysztof Kuczera
Departments of Chemistry and Molecular Biosciences
The University of Kansas
2010 Malott Hall
Lawrence, KS 66045
Tel: 785-864-5060 Fax: 785-864-5396 email: kkucz...@ku.edu
http://oolung.chem.ku.edu/~kuczera/home.html
--
gmx-users mailing listgmx-users@gromacs.org
:
Krzysztof Kuczera wrote:
Hi GMXers,
I am interested in simulating blocked peptides with CHARMM (and other
force fields), using gromacs-4.5, and would appreciate some help from
more experienced GROMACS users on details.
To test things out I made a stab at creating an ACE N-terminal patch
--
Krzysztof Kuczera
Departments of Chemistry and Molecular Biosciences
The University of Kansas
2010 Malott Hall
Lawrence, KS 66045
Tel: 785-864-5060 Fax: 785-864-5396 email: kkucz...@ku.edu
http://oolung.chem.ku.edu/~kuczera/home.html
ala5_alpha.pdb
Description: Protein Databank data
--
gmx
--
Krzysztof Kuczera
Professor
Departments of Chemistry and Molecular Biosciences
The University of Kansas
2010 Malott Hall
Lawrence, KS 66045
Tel: 785-864-5060 Fax: 785-864-5396 email: kkucz...@ku.edu
http://oolung.chem.ku.edu/~kuczera/home.html
--
gmx-users mailing listgmx-users
GLY-NH3+ and GLY-COO- as well ...
Could someone suggest a fix for this ?
Regards
Krzysztof
--
Krzysztof Kuczera
Departments of Chemistry and Molecular Biosciences
The University of Kansas
2010 Malott Hall
Lawrence, KS 66045
Tel: 785-864-5060 Fax: 785-864-5396 email: kkucz...@ku.edu
http
up with incorrect charge and qtot
is not an integer
Without the '-inter', the system gets GLY-NH3+ and GLY-COO- as well ...
Could someone suggest a fix for this ?
Regards
Krzysztof
--
Krzysztof Kuczera
Departments of Chemistry and Molecular Biosciences
The University of Kansas
2010 Malott
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