ypically solves bad atomic clashes.
-Justin
--
============
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/
pproach, for instance "pbc = xy" for an infinite
z-dimension. There are limitations to this approach, as stated in the manual,
but it may be more sound.
-Justin
--
============
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
/Mixed_Solvents
-Justin
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
to cluster???please
let me know and i am struggling with this from past 1month.Please tell
me how to solve this
The error says you are "out of quota," i.e. out of disk space.
-Justin
--
====
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Sch
x27;low' in the above table ? Should I obtain value for the initial
Ca-Ca distance between my residues from the initial structure? How I
could do it?
See Figure 4.13 and equations 4.79 in the manual. r0 = low, r1 = up1, and r2 =
up2.
-Justin
--
=========
s for producing coordinate files. See, for instance:
http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#Sources
-Justin
--
====
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia
Steven Neumann wrote:
On Mon, Mar 12, 2012 at 11:06 AM, Justin A. Lemkul <mailto:jalem...@vt.edu>> wrote:
Steven Neumann wrote:
On Sun, Mar 11, 2012 at 10:13 PM, Justin A. Lemkul
mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mail
specific question related to what you can't find or don't understand.
-Justin
--
============
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu |
Steven Neumann wrote:
On Sun, Mar 11, 2012 at 10:13 PM, Justin A. Lemkul <mailto:jalem...@vt.edu>> wrote:
Steven Neumann wrote:
Hi Justin,
As you advised I reduced number of my windows and I obtined
histogram:
http://speedy.sh/2b9dT/hi
gmentation fault
Your simulation crashed. The fact that it did so immediately suggests
inadequate energy minimization and/or equilibration.
http://www.gromacs.org/Documentation/Terminology/Blowing_Up
-Justin
--
====
Justin A. Lemkul
Ph.D. Candidate
ICTA
wo are the
most likely possibilities.
-Justin
--
====
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Page
erlap is likely fine, you just may need a bit more sampling in each window to
smooth things out. Also make use of the error estimates that g_wham can
provide; they can be quite informative (and necessary).
-Justin
--
====
Justin A. Lemkul
Ph.D. Candidate
o achieve completely different tasks.
If you want a specific answer to solve a specific task, ask a specific question.
-Justin
--
========
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Bla
r
than following the step-by-step instructions provided online.
-Justin
--
============
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
-0.613 0.255 0. 0. 0.
3DRGCAA 13 0.495 -0.175 -0.072 0. 0. 0.
3DRGCAB 14 0.483 -0.311 -0.143 0. 0. 0.
Thanks
Nahid
--
========
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Sch
-Justin
--
====
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
--
gmx-users ma
;Great Red Owns Many ACres of Sand "
solvent configuration contains 60 atoms in 10 residues
Killed
Would you please help me?
Thanks alot
Regards
Saly
--
============
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department
lp me?
Thanks
Saly
--
============
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
===
Dialing Pretty wrote:
Dear All,
Is the following force field still practical or not?
GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
Is there some reason to suggest otherwise?
-Justin
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral
gle and force constant. They will be looked up in ffbonded.itp.
-Justin
Greetings
Lara
- Ursprüngliche Message -
Von: Justin A. Lemkul
An: Discussion list for GROMACS users
CC:
Gesendet: 21:04 Mittwoch, 7.März 2012
Betreff: Re: [gmx-users] Missing Interactions in [ angles
ce) or their
bonds are flexible. Thus, I am not really using any constraints, unless
freeze groups count as constraints. However, I am not sure what this means
as far as what to set "continuation" to in a2.mdp and a3.mdp.
The "continuation" keyword applies to bond co
4)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---
"Act like Prometheus would" (Gogol Bordello)
: Cannot allocate memory
--
==========
and rename 'HN' to 'H'
and re-compile a test .tpr file. Try g_helix again using this .tpr file. If it
works (or doesn't), please report back.
-Justin
--
====
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
erate a suitable grid of a
smaller number of molecules, say a few hundred, then use genbox -cs -maxsol to
fill a new box with the desired number of solvent molecules.
-Justin
--
====
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
think you can do it with:
g_rdf -com -rdf mol_com
-Justin
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http
,
or otherwise using g_select to find OW atoms within whatever your distance is,
since the count of OW will be the number of molecules of water within that distance.
-Justin
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
tions in each selection for each
frame."
From trjorder -h:
"With option -nshell the number of molecules within a shell of radius -r
around the reference group are printed."
Thus the two output files should not be equivalent.
-Justin
--
============
J
utput of grompp for the actual restraint distances that mdrun will
interpret. They are printed to the screen.
-Justin
--
========
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalem
dex groups that tell you which
atoms satisfy the given criteria. With trjorder, the coordinates of those atoms
are reordered such that they are listed in sequence in the new trajectory.
-Justin
--
============
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scho
-okt -okr
Note that information derived from velocities does not correct for the presence
of constraints. You'll have to do that yourself.
-Justin
--
====
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Bi
body
bonded interaction? I cannot seem to find this in the manual.
All of these messages have to do with the configuration of the DD cells. The
details are explained in the Gromacs 4 paper:
http://pubs.acs.org/doi/abs/10.1021/ct700301q
-Justin
--
====
-Justin
--
====
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Perso
x27; ' so it is interpreted as a
single string. As it stands, the words resname, SOL, and, etc are being
interpreted as arguments, which they are not.
-Justin
--
============
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of B
the parametrization are out of a supporting information of a paper that did MD with my molecule.
The System is my molecule (isoalloxazine) in water.
Do you want to see my .rtp file?
Thanks you for helping me.
Greetings
Lara
- Ursprüngliche Message -
Von: Justin A. Lemkul
An
taG. Moreover, in the absence of any error estimates, you
can't make any conclusions about these data. g_wham can generate error bars for
you; I'd suggest you do it.
-Justin
Shahid Nayeem
On Tue, Feb 28, 2012 at 7:44 PM, Justin A. Lemkul mailto:jalem...@vt.edu>> w
is (and always has been) buggy.
-Justin
--
========
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.bioche
actly, the periodicity is not being handled correctly. Presumably you're
dealing with an infinite sheet (thus bonds extend across periodic boundaries),
and thus you need to set "periodic_molecules = yes" in the .mdp file.
-Justin
--
Jus
pology. If there
is a bonded interaction referenced in the topology that does not exist in
ffbonded.itp, grompp will fail with a fatal error.
-Justin
--
========
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistr
to topology but what could be
the reason for this problem?
What exactly is missing? By default, pdb2gmx generates all possible angles.
-Justin
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
type of proper dihedral) while the second indicates
improper dihedrals.
-Justin
--
============
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540
-Justin
--
====
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
--
gmx-users ma
above is syntactically correct, so it's not what you typed ;)
Check carefully for typos and spacing, particularly if you have mis-spaced or
omitted the -o flag, which would cause the file name to be incorrectly interpreted.
-Justin
--
====
Justin A. L
eed (substituting -extend or -until, whichever you prefer, though
-until is a bit more reliable where rounding is concerned) are here:
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#Version_4
-Justin
--
====
Justin A. Lemkul
Ph.D. Candidate
IC
command to reinstiate the gromacs
after it has stopped for example at 0.1 ns, which means I will restart
from 0.1 ns?
http://www.gromacs.org/Documentation/How-tos/Doing_Restarts#Version_4.x
-Justin
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral
indicates there is a dihedral for which parameters do not exist.
-Justin
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http
re the error is.
-Justin
--
============
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/
Justin A. Lemkul wrote:
Lara Bunte wrote:
Hello
Is this em.mdp file correct for a simple MD simulation?
integrator = steep
nsteps = 200
nstlist = 10
You should set nstlist=1 for energy minimization (which is not, by
definition, MD).
Hit "send" too soon...
You have also
rvdw = 1.0
nstenergy = 10
Thanks for help
Greetings
Lara
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http
!
Steven
--
====
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
--
gmx-users ma
ation.
How and where do I give this information to gromacs? Could you give me just one
line example syntax?
Look in ffnonbonded.itp, in the [atomtypes] directive. The format and contents
of this directive are explained in the manual.
-Justin
--
====
Jus
previously
conducted using constraints, so in that case, the distinction between the two is
probably irrelevant. You should do whatever makes the most physical sense in
your case.
-Justin
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT
ginal publications or
any that refer to modifications of the original parameter set. Details can be
sketchy depending on the force field, so be prepared to invest significant time
in this endeavor.
-Justin
--
====
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Sc
ustin
--
====
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
--
gmx-users mailing list
gs you think are problems."
Unless you understand the exact implications of overriding these warnings, you
shouldn't be blindly pushing forward. As the warning states, your time step is
too long to be stable in the absence of constraints.
-Justin
--
============
x27;ve seen in AMBER tutorials?
The atom names used are standard nomenclature for amino acids.
Also I am interested in knowing on how the topology files are created
from scratch?
Sorry, I don't understand what you mean here.
-Justin
--
==========
chain. TPOH
is the -1 form of the phosphate and thus there is a proton on the phosphate group.
-Justin
--
====
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]v
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
--
gmx-users mailing list
. Check gmx.ff/aminoacids.rtp for a complete description of
each of the 8 possible columns and the order that they must follow.
-Justin
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia
or
interactions that do not follow standard combination rules, but that's not
necessarily relevant here.
-Justin
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia
for each simulation). More can be used, but
it must be a multiple of the number of simulations, as the error message indicates.
-Justin
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
--
gmx-users mailing listgmx-users
Steven Neumann wrote:
On Thu, Mar 1, 2012 at 5:43 PM, Justin A. Lemkul <mailto:jalem...@vt.edu>> wrote:
Steven Neumann wrote:
On Thu, Mar 1, 2012 at 3:58 PM, Steven Neumann
mailto:s.neuman...@gmail.com>
<mailto:s.neuman...@gmail.com &
other Gromacs tools) has done its job correctly.
-Justin
--
====
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.v
Steven Neumann wrote:
On Thu, Mar 1, 2012 at 3:58 PM, Steven Neumann <mailto:s.neuman...@gmail.com>> wrote:
On Thu, Mar 1, 2012 at 3:32 PM, Steven Neumann
mailto:s.neuman...@gmail.com>> wrote:
On Thu, Mar 1, 2012 at 2:55 PM, Justin A. Lemkul
voke the opposite (which is true for all Gromacs
options), the syntax is genion -norandom.
-Justin
--
============
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
-Justin
--
====
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
--
gmx-users ma
reciate.
Thank you,
Steven
--
========
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
===
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
--
gmx-users mailing listgmx-users
k you!
Bo
--
====
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Perso
presumably) repetitive topology for a relatively large
particle. You may or may not need to invoke specbond.dat for cross-links, as
pdb2gmx can deal only with linear species via .rtp entries; other bonds are
introduced with specbond.dat.
-Justin
On Tue, Feb 28, 2012 at 5:46 PM, Justin
Steven Neumann wrote:
On Tue, Feb 28, 2012 at 6:33 PM, Justin A. Lemkul <mailto:jalem...@vt.edu>> wrote:
Steven Neumann wrote:
I run energy minimization of my protein with implicit solvent:
constraints = none
integrato
://www.gromacs.org/Documentation/How-tos/Polymers
-Justin
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http
to
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field.
If the molecule is a standalone species like a ligand, solvent, etc then all
you have to do is #include an .itp file in the system topology.
-Justin
--
Justin A. Lemkul
an in vacuo minimization work (i.e., just turn off the GB parts)?
-Justin
--
====
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
h
compatible with DD.
-Justin
--
========
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
===
fields. If you are unsatisfied with the
chosen protonation, there are command line options to interactively change the
protonation state of any titratable residues.
-Justin
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
uld be
unusual. It's not likely a consequence of bad parameterization, rather bad
construction of the necessary input files.
-Justin
--
============
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia
opers] for improper
dihedrals - in ffbonded.itp you would specify parameters for the impropers
within a [dihedraltypes] block and specifying the correct function type for the
interaction.
-Justin
--
====
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Sch
f the physical model. It can be
argued that rigid bonds are a more realistic representation of ground state
bonds, in addition to making the simulations more efficient.
-Justin
--
============
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT T
n interpretation of the contents.
-Justin
--
========
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.be
f the system. Looking at the interactions between your proteins,
the stability of those proteins, etc. is far more informative, like you would
for any simulation (even those that do not make use of the pull code).
-Justin
--
====
Justin A. Lemkul
Ph.D. Cand
g/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
========
Justin A. Lemk
-noappend and just concatenate your output later. Something in the
filesystem thinks your .log file is still in use.
-Justin
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
ong environment variable. Use MPICC, not CC.
-Justin
--
========
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.b
or with similarly with
autoconf, use the MPICC environment variable to point to the mpicc of choice.
-Justin
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at
ts to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>.
Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists
<http://www.gromacs.org/Support/Mailing_Lists>
--
=
is commonplace, but only in
certain situations is it necessary to undo their effects. It does not sound to
me like this is the case in your situation.
-Justin
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of
ustin
--
====
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
--
gmx-
Juliette N. wrote:
On 24 February 2012 16:52, Justin A. Lemkul <mailto:jalem...@vt.edu>> wrote:
Juliette N. wrote:
On 23 February 2012 21:18, Mark Abraham mailto:mark.abra...@anu.edu.au>
<mailto:mark.abra...@anu.edu.__au
<mailto:mark.
instead of PME, which can change the way electrostatics are handled if using the
latter method. Probably someone, somewhere along the way, has published
recommendations for normal use in whatever type of system you're dealing with.
-Justin
--
============
S formed between O and H atoms.
Where is my mistake?
Probably the atom names are wrong. This is a VMD question, so you're better off
posting to the VMD mailing list for help on such topics.
-Justin
--
============
Justin A. Lemkul
Ph.D. Candidate
ICTAS D
onger simulations to do so, but you
can start by examining the physical properties of each window. What you're
looking for is up to you, based on your knowledge of the system at hand.
-Justin
--
====
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Sch
.
-Justin
--
====
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
--
gmx-users mailing l
as necessary).
-Justin
--
============
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
w any reasonable conclusions.
-Justin
--
====
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/j
erminology/Periodic_Boundary_Conditions
-Justin
--
====
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Perso
fist
1ns run for equilibriation.
OK, so how did you decide that 10 ns was sufficient in each window?
-Justin
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul
le to do pKa
estimates, for instance:
http://biophysics.cs.vt.edu/
-Justin
--
====
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
ments you want to
consider, you have to create complementary groups for all the rest, i.e.:
enerygrps = fragment Protein_not_fragment sol_fragment SOL_not_sol_fragment
-Justin
--
====
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Tr
801 - 900 of 7481 matches
Mail list logo