parto haghighi wrote:
Dear GMX users,
when I want to correct charge group of one molecule I have to do
calculate its free energy.
I did this work by applying 6th gromacs tutorial.
In this tutorial user has to assign 0 value in topology:
[ atoms ]
; nr type resnr residue atom cgn
Hello, I am a beginner of Gromacs, and I am working with enzyme that contains
two Cu2+ ions in the active site. I have found two solution to treat copper
ions and surrounding His residues. First solution is adding position restrain
to these ions, while the second one is defining bonds between co
Hi,
I sent this email few weeks back and thought sending it again in case someone
can give some opinion.
I have a technical question regarding feasibility of combining replica
exchange with umbrella sampling or any other pulling simulations in gromacs.
Since the umbrella sampling or any other
Hi Mark (and all)
Thanks for the response. I ran ./configure --disable-threads this time.
./configure went fine but again upon doing Make I have received a new error:
Creating library file: .libs/libmd.dll.a
.libs/fft5d.o:fft5d.c:(.text+0x140f): undefined reference to
`_fftwf_plan_guru_d
ft
You do not need to fix the copper in the calculation. There are must be some
negative charged residues around the copper. Therefore, the copper will located
at the place where it should be.
regards.
--
Xianqiang Sun
Email: xianqi...@theochem.kth.se
Division of Theoretical Chemistry and Bio
Hi all,
I want to know if I can
implement the CHARMM27 parameter file in gromacs-4.0.7
thanks
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/
xianqiang wrote:
You do not need to fix the copper in the calculation. There are must be
some negative charged residues around the copper. Therefore, the copper
will located at the place where it should be.
I agree that a position restraint on copper is not appropriate, but I strongly
dis
On 4/01/2012 5:04 AM, Rashek Kazi wrote:
Hi Mark (and all)
Thanks for the response. I ran ./configure --disable-threads this
time. ./configure went fine but again upon doing Make I have received
a new error:
Creating library file: .libs/libmd.dll.a
.libs/fft5d.o:fft5d.c:(.text+0x140f): undef
On 4/01/2012 6:49 AM, najwa drici wrote:
Hi all,
I want to know if I can implement the CHARMM27 parameter file in
gromacs-4.0.7
Yes, you can implement CHARMM27, but no you will not be able to use the
files from GROMACS 4.5 without heavy modification.
Mark
--
gmx-users mailing listg
I used VMD to process a gro file and wrote it to pdb, because VMD can't
write gro files. Because the # of residues exceeds , it numbered the
remaining residues in the PDB in 4 bit hex. Editconf will not convert the
hex numbered residue ids back to decimal (it just truncates anything past
th
Thanks for all your replies. I want to know this can be done in gromacs or
not - using REMD with structure based models generated from SMOG server to
study protein folding and unfolding ??. Also, I have a question about how
to determine the exchange probablities for a particular REMD experiment
an
On 4/01/2012 12:30 PM, Peter C. Lai wrote:
I used VMD to process a gro file and wrote it to pdb, because VMD can't
write gro files. Because the # of residues exceeds , it numbered the
remaining residues in the PDB in 4 bit hex. Editconf will not convert the
hex numbered residue ids back to d
On 4/01/2012 12:35 PM, bharat gupta wrote:
Thanks for all your replies. I want to know this can be done in
gromacs or not - using REMD with structure based models generated from
SMOG server to study protein folding and unfolding ??.
Well, it can be done, but you probably don't have enough comp
Thanks for the reply. Since I need to study the effect of beta-hairpin turn
design on protein folding . I thought that first unfolding and then
refolding would give the change in folding time. As you told that to do
such a task would require large computational power. Is there any other
method in M
On 2012-01-04 12:46:09PM +1100, Mark Abraham wrote:
> On 4/01/2012 12:30 PM, Peter C. Lai wrote:
> > I used VMD to process a gro file and wrote it to pdb, because VMD can't
> > write gro files. Because the # of residues exceeds , it numbered the
> > remaining residues in the PDB in 4 bit hex.
On 4/01/2012 1:07 PM, Peter C. Lai wrote:
On 2012-01-04 12:46:09PM +1100, Mark Abraham wrote:
On 4/01/2012 12:30 PM, Peter C. Lai wrote:
I used VMD to process a gro file and wrote it to pdb, because VMD can't
write gro files. Because the # of residues exceeds , it numbered the
remaining re
Actually i know people using Go-models to study protein folding for proteins as
large as 300 aa. Now, in these cases you need to use biasing potentials and not
temperature exchages (maybe both?). In principle, the REMD will help you with
the comformational exchange but it also includes a new le
Hello:
I submit MD jobs to cluster with the following scrips:
# @ job_name = gromacs_job
# @ class = kdm-large
# @ account_no = G07-13
# @ error = gromacs.out
# @ output = gromacs.out
# @ environment = COPY_ALL
# @ wall_clock_limit = 2:00:00
# @ notification = error
# @ notify_user = alb...@ic
Albert wrote:
Hello:
I submit MD jobs to cluster with the following scrips:
# @ job_name = gromacs_job
# @ class = kdm-large
# @ account_no = G07-13
# @ error = gromacs.out
# @ output = gromacs.out
# @ environment = COPY_ALL
# @ wall_clock_limit = 2:00:00
# @ notification = error
# @ noti
On 2012-01-04 01:21:01PM +1100, Mark Abraham wrote:
> On 4/01/2012 1:07 PM, Peter C. Lai wrote:
> > On 2012-01-04 12:46:09PM +1100, Mark Abraham wrote:
> >> On 4/01/2012 12:30 PM, Peter C. Lai wrote:
> >>> I used VMD to process a gro file and wrote it to pdb, because VMD can't
> >>> write gro files
On 4/01/2012 2:19 PM, Peter C. Lai wrote:
On 2012-01-04 01:21:01PM +1100, Mark Abraham wrote:
On 4/01/2012 1:07 PM, Peter C. Lai wrote:
On 2012-01-04 12:46:09PM +1100, Mark Abraham wrote:
On 4/01/2012 12:30 PM, Peter C. Lai wrote:
I used VMD to process a gro file and wrote it to pdb, because
On 2012-01-04 02:54:28PM +1100, Mark Abraham wrote:
> On 4/01/2012 2:19 PM, Peter C. Lai wrote:
> > On 2012-01-04 01:21:01PM +1100, Mark Abraham wrote:
> >> On 4/01/2012 1:07 PM, Peter C. Lai wrote:
> >>> On 2012-01-04 12:46:09PM +1100, Mark Abraham wrote:
> On 4/01/2012 12:30 PM, Peter C. Lai
On 4/01/2012 2:59 PM, Peter C. Lai wrote:
On 2012-01-04 02:54:28PM +1100, Mark Abraham wrote:
On 4/01/2012 2:19 PM, Peter C. Lai wrote:
On 2012-01-04 01:21:01PM +1100, Mark Abraham wrote:
On 4/01/2012 1:07 PM, Peter C. Lai wrote:
On 2012-01-04 12:46:09PM +1100, Mark Abraham wrote:
On 4/01/20
Hello
I am trying to adjust compound LJ parameter in oplsaa (sigma&epsilon) and
also in Gromos (C6 and C12) forcefield for comparison. The original
ffnonbonded.itp file in oplsaa.ff has no pair potential listed. While the
original ffnonbonded.itp file in gromos**.ff listed all the pair
potentials.
On 4/01/2012 4:43 PM, XUEMING TANG wrote:
Hello
I am trying to adjust compound LJ parameter in oplsaa (sigma&epsilon)
and also in Gromos (C6 and C12) forcefield for comparison. The
original ffnonbonded.itp file in oplsaa.ff has no pair potential
listed. While the original ffnonbonded.itp file
I'd appreciate any help --
I'm trying to model a small (~ 20-carbon ) molecule linked to a diamond
surface. I got the diamond surface with >1500 atoms working fine all
the way through to the MD simulation and it looks great. But I'm
getting stuck on the molecule, which is not a protein but
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