David,
Thanks for your reply. These are bonded interactions, but there are
some angle-angle cross terms involving products of cosines of angles. I
could probably try to convert them to one of the available bonded
functions.
Daniel
___
gmx-users
Cherry Y. Yates wrote:
Dear Mark,
Thanks for your help, I followed you instruction, and I can get stable
temperature after I remove the temperature coupling. In this case I used
the flexible spc itp file. However if I use a rigid spc.itp, after
remveing the temperature coupling, the system t
Hi,
I have been a bit confused by the g_rmsf output. In the
manual, it says that “g_rmsf computes the root mean square fluctuation
(RMSF, i.e. standard deviation) of atomic positions after first fitting to a
reference frame.” But what *is*
the reference frame?
I assume that this out
Dear Mark,Thanks for your help, I followed you instruction, and I can get stable temperature after I remove the temperature coupling. In this case I used the flexible spc itp file. However if I use a rigid spc.itp, after remveing the temperature coupling, the system temperature is shooting up from
Dear Dr Spoel Thanks for the prompt reply. Yes I did shuffle the trajectories. I shall try to recompute after deshuffling the trajectories. Thanks again, Sincerely Regards RamaDavid van der Spoel <[EMAIL PROTECTED]> wrote: Rama Gullapalli wrote:> Hi GMX ers,> I posted this question earlier, b
Rama Gullapalli wrote:
Hi GMX ers,
I posted this question earlier, but did not receive a reply. Hope to get
an answer this time around.
I was wondering what could be the origin of a spike at close distances
when I compute the RDF of N-P atoms in a lipid bilayer system (<0.25
nm) I tried us
Hi GMX ers, I posted this question earlier, but did not receive a reply. Hope to get an answer this time around.I was wondering what could be the origin of a spike at close distances when I compute the RDF of N-P atoms in a lipid bilayer system (<0.25 nm) I tried using -cut option and also
Thanks, David. i appreciate your response.o.David van der Spoel <[EMAIL PROTECTED]> wrote: Omololu Akin-Ojo wrote:> Hi,> > i use GROMACS & i like it because it is so fast. But, i would like to > know if GROMACS "cut corners" ? Otherwise, why is it is so fast?> if you have a fortran compiler on an O
Maik,
I'm trying to do a simple FEP within a simple protein, which seems to
make things simple...but as you may expect...it is anything else than that.
What I'm trying to do is morphing a Tyrosine into a Phenylalanine in OPLSAA.
Therefore the CZ is changed from the type of TYR to the type of
Mauricio,
Exactly: I`d want to calculate "dG/dl for some particular component of
the energy". Why? I did 2 FEPs, so I have two Delta_Gs for a mutations in
2 states: folded and unfolded. Both Delta_Gs are positive values. The
difference between them (Delta_Delta_G) is the value I was looking for.
Maik Goette wrote:
Update:
Checked it with the Amber99 port. Same strange habit. It occured with
another protein (system), too.
please submit a bugzilla.
--
David.
David van der Spoel, PhD, Assoc. Prof., Molecular Bio
Omololu Akin-Ojo wrote:
Hi,
i use GROMACS & i like it because it is so fast. But, i would like to
know if GROMACS "cut corners" ? Otherwise, why is it is so fast?
if you have a fortran compiler on an Opteron box, GROMACS does not use
the assembly loops. Right? So, why is it blazingly fast?
o
Hi,i use GROMACS & i like it because it is so fast. But, i would like to know if GROMACS "cut corners" ? Otherwise, why is it is so fast?if you have a fortran compiler on an Opteron box, GROMACS does not use the assembly loops. Right? So, why is it blazingly fast?o.
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> Hey all
>
> I'm trying to do a simple FEP within a simple protein, which seems to
> make things simple...but as you may expect...it is anything else than
> that.
>
> What I'm trying to do is morphing a Tyrosine into a Phenylalanine in
> OPLSAA.
> Therefore the CZ is changed from the type of TY
Update:
Checked it with the Amber99 port. Same strange habit. It occured with
another protein (system), too.
Regards
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel. : ++49 5
Tanks David
Exactly: I`d want to calculate "dG/dl for some particular component of
the energy". Why? I did 2 FEPs, so I have two Delta_Gs for a mutations in
2 states: folded and unfolded. Both Delta_Gs are positive values. The
difference between them (Delta_Delta_G) is the value I was looking f
Hi Harpreet,
Regarding the message "invalid order ...", check the archives of this
mailing list. Further note that you shouldn't use the gmx (ffgmx)
force field, but should choose one of the Gromos force fields (united
atom), OPLS or Encad (all-atom).
Specific to your problem is that there is a
Hey all
I'm trying to do a simple FEP within a simple protein, which seems to
make things simple...but as you may expect...it is anything else than that.
What I'm trying to do is morphing a Tyrosine into a Phenylalanine in OPLSAA.
Therefore the CZ is changed from the type of TYR to the type of
harpreet singh wrote:
Fatal error:
Atom O1P in residue FAD 1 not found in rtp entry with 61 atoms
while sorting atoms
On comparing topology file (ffgmx.rtp) for FAD entry i was surpried to
see that it has atom type enteries OP1, OP2 instead of O1P, O2P in
downloaded PDB file (fad.pd
if i were you, i would rather adapt my pdb file to an existing forcefield as
ffgmx, than trying to generate a new forcefield that fits to your pdb with
prodrug. the first option seems much easier to me. what i mean is, if you
change the names of you FAD atoms to the ones you see in the *rtp they
Hi All,
I am new to this package and want your help. I am trying to use GROMACS to
study energy minimization and molecular dynamics for FAD molecule. I am
having the following problems.
1. I tried to run pdb2gmx for PDB file for FAD downloaded from
http://www.ebi.ac.uk/msd-srv/msdchem/cgi-
...msms can calculate the surface of an atom list (generated from a pdb).
This surface is triangulated and calculating the volume from a triangulated
surface should be very easy.
Regards
Martin
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On Tuesday 07 November 2006 08:46, David van der Spoel wrote:
> Tsjerk Wassenaar wrote:
> > Hi Alex,
> >
> > I think you're best off describing the wall with particles. You can
> > freeze them to a specific position (make it a freeze-group) and set
> > all interactions between them to zero. You can
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