Louic Vermeer wrote:
In my previous message I used "all-atom" in stead of "united-atom" twice: in
the part about the SDS topology and again between the parentheses in my third
question. That's probably very confusing, so I made the corrections in my
quoted message below.
Sorry for the inconven
Does anybody know if grompp uses the forces from a loaded .trr file in
order to create the .tpr file?
My interest is based on the fact that trjconv does not appear to
deshuffle forces as it does for coordinates and velocities as
presented in a recent gromacs thread starting here:
http://w
Alan Dodd wrote:
Thankyou - a few hundred ps was quite doable. Temperature is (fortunately!)
consistent between groups to well within a couple of degrees, which is probably
fine, but I just want to check that the temperatures from groups in g_traj are
directly comparable with each other? The
I am attempting to pull a ligand through a channel protein. I have setup the
umbrella sampling code and it seems to be working just fine except I get
large jumps in the
deviation of each pulled group from its restrained position at 1 ps
intervals. I am pulling three groups all relative to the backb
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Best wishes
Hi Landry,
well: make_hole just works with Gromacs version 3.1.4 - download this
old version from the gromacs homepage, start from the beginning, and
everything should work fine.
J'espere que ca t'aide
Steffen
> Hi
>
> I try to install gromacs with make_hole utility so I download the
> gromacs-3.3.
Hi
I try to install gromacs with make_hole utility so I download the
gromacs-3.3.2.tar.gz, I uncompress it, I download the mdrun_make_hole.tar.gz and
uncompress it in the gromacs folder. After the ./configure command which
completed successfully, I run the make command and I get the following err
[EMAIL PROTECTED] wrote:
Dear Mark,
Thanks a lot for your reply.
Default was 1.6 angstrom and when I change gradually till 2.5 angstrom then
structure looks similar to original structure.
I have again checked in my top and mdp files for include statement.
I have define = -DFLEXIBLE in my mdp
Thank you so much.
On Jan 30, 2008 2:57 AM, Tsjerk Wassenaar <[EMAIL PROTECTED]> wrote:
> Hi Myunggi Yi,
>
> >
> > Mixing force fields is an intrinsically bad idea. See
> > http://wiki.gromacs.org/index.php/Parameterization
> >
>
> I second that...
>
> > > Is it possible to turn off dihedral ene
Dear Chris,
Thanks for your help.
I have also tried the "comm_grps = System" option, and did energy
minimization but after that also water molecular looked like the previous
case (Figure-B, in my previous post).
Regards,
Alok
> >Dear All,
> >
> >I am doing the simulation of POPE lipid + Prote
Sorry again,
I just checked in case of TIP4P water molecules there is separate section
[ constraints ] which is used if we do not use FLEXIBLE water. It does
not uses SETTLE algorithm for constraining water molecules (correct me if
I am wrong). Sorry for my previous mail.
Regards,
Alok
> Dea
In my previous message I used "all-atom" in stead of "united-atom" twice: in
the part about the SDS topology and again between the parentheses in my third
question. That's probably very confusing, so I made the corrections in my
quoted message below.
Sorry for the inconvenience.
Louic
> Hi eve
Dear Mark,
Thanks a lot for your reply.
Default was 1.6 angstrom and when I change gradually till 2.5 angstrom then
structure looks similar to original structure.
I have again checked in my top and mdp files for include statement.
I have define = -DFLEXIBLE in my mdp file
in my top file I have
Hi everybody,
I want to do a refinement of an NMR structure, using NOE restraints. I
want to do this in SDS, using an SDS topology file[1] that was designed
for gromacs, but there are no explicit hydrogen atoms. I think it's not
a good idea to simulate a peptide with explicit hydrogens in comb
Thankyou - a few hundred ps was quite doable. Temperature is (fortunately!)
consistent between groups to well within a couple of degrees, which is probably
fine, but I just want to check that the temperatures from groups in g_traj are
directly comparable with each other? They're not the same a
If the transformation can not be analytical, I could fit (numerically)
the parameters of the Ryckaert-Belleman potential to the function that
results from the original one... Although this is not probably the best
way of using the force field as originally proposed, the difference
should be negligi
>
> hello users
> I am starting a membrane protein simulation. I had some missing residues
> in the protein which have been added now. Should I minimise in vaccum
> before insertion of the protein in bilayer?
That depends how "bad" the new residue coordinates are, and whether vacuum
EM is better t
Quoting pragya chohan <[EMAIL PROTECTED]>:
>
> hello users
> I am starting a membrane protein simulation. I had some missing residues in
> the protein which have been added now. Should I minimise in vaccum before
> insertion of the protein in bilayer?
Couldn't hurt, but probably not necessary. R
> Ángel Piñeiro wrote:
>> Dear David
>> I have taken a look to the manual (version 3.3) and I haven't found
>> information about how to tabulate bonded potential functions (it seems
>> that Ran is right). On the other hand, what do you mean exactly with
>> adding two dihedrals?
> It could well be t
> Date: Wed, 30 Jan 2008 11:59:30 +0100
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: RE: RE : FEP : separating components of dgdl (Berk Hess)
>
>
> Hi,
>
> After some tedious work to locate the problem, I just realized that the term
Hi,
After some tedious work to locate the problem, I just realized that the term
for bonds is missing in the log file !
It could account for the difference, but in fact another error occured :
(Note : I am using amber99 ports )
In my system, I defined an atom DUM with just the same parameters
Dear David
I have taken a look to the manual (version 3.3) and I haven't found
information about how to tabulate bonded potential functions (it seems
that Ran is right). On the other hand, what do you mean exactly with
adding two dihedrals?
Angel Pineiro.
> > Date: Tue, 29 Jan 2008 19:18:20 +01
hello users
I am starting a membrane protein simulation. I had some missing residues in the
protein which have been added now. Should I minimise in vaccum before insertion
of the protein in bilayer?
Another question : Is it necessary to do simulation in water before inserting
protein nto bilay
Ángel Piñeiro wrote:
Dear David
I have taken a look to the manual (version 3.3) and I haven't found
information about how to tabulate bonded potential functions (it seems
that Ran is right). On the other hand, what do you mean exactly with
adding two dihedrals?
It could well be that you'll have
Dear David
I have taken a look to the manual (version 3.3) and I haven't found
information about how to tabulate bonded potential functions (it seems
that Ran is right). On the other hand, what do you mean exactly with
adding two dihedrals?
Angel Pineiro.
> Date: Tue, 29 Jan 2008 19:18:20 +0100
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