Dear Gromacs Users,
I want to calculate dihedral angle distribution for 9 dihedral angles in
aliphatic chain of my molecule. I created the index file giving the command
make_ndx -f run.gro -o dihedral.ndxThen I typed,a C13 a C14 a C15 a C16a C14 a
C15 a C16 a C17a C15 a C16 a C17 a C18a C16 a C
Dear all,
I am trying to do REMD simulation in different cosolvents. I have generated
temperatures using temperature genrating tools but it gives different
number of temperatures in different solvents with exchange probability of
0.25. Is it fair to do remd with different replicas? In what way it w
Hi,
I have input structure from my last simulation. The box is 12nm long in Z
axis. There is a wall and sheet in z=3 and z=8( so z=~ 0 to 3 and z=~ 8 to
12 is empty) . I want to add solvent between z=3-8. How can i do that?
The problem is that i cant adjust wall and sheet( z coordination) to star
Dear all,
I wonder if the topolbuild can provide the gromos 54A7 (gmx54a7) FF?
Regards,
Alex
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One of the recurring questions on the list seems to be how to define
residue protonation states non-interactively in pdb2gmx input. The
interactive options are a bit of a nightmare to use. Could pdb2gmx be
modified to optionally read the residue types from the PDB file
itself? The user wo
On 4/16/18 5:58 AM, rose rahmani wrote:
Hi,
I have input structure from my last simulation. The box is 12nm long in Z
axis. There is a wall and sheet in z=3 and z=8( so z=~ 0 to 3 and z=~ 8 to
12 is empty) . I want to add solvent between z=3-8. How can i do that?
The problem is that i cant ad
On 4/16/18 7:07 AM, mhuht...@abo.fi wrote:
One of the recurring questions on the list seems to be how to define
residue protonation states non-interactively in pdb2gmx input. The
interactive options are a bit of a nightmare to use. Could pdb2gmx be
modified to optionally read the residue ty
On 4/16/18 3:07 AM, Anjana Jayasinghe wrote:
Dear Gromacs Users,
I want to calculate dihedral angle distribution for 9 dihedral angles in
aliphatic chain of my molecule. I created the index file giving the command
make_ndx -f run.gro -o dihedral.ndxThen I typed,a C13 a C14 a C15 a C16a C14 a
On 4/15/18 9:22 PM, sunyeping wrote:
Dear everyone,
Do you have a tutorial of building a virus lip bilayer envelope with its
glycoproteins for MD simulation? Recenetly some MD simulation have done with
the envelope of some viruses such as influenza virus (Reddy et al., 2015) and
dengue vir
Thank you so much.
You mean first use gmx solvate, then delete the Sol molecules which i dont
need them?
So trjorder can fix the rest, yes?
On Mon, 16 Apr 2018, 16:26 Justin Lemkul, wrote:
>
>
> On 4/16/18 5:58 AM, rose rahmani wrote:
> > Hi,
> >
> > I have input structure from my last simulatio
On 4/16/18 8:51 AM, rose rahmani wrote:
Thank you so much.
You mean first use gmx solvate, then delete the Sol molecules which i dont
need them?
Yes.
So trjorder can fix the rest, yes?
No, but trjconv can save what you want based on an index group from gmx
select.
-Justin
On Mon, 16
On Apr 16, 2018, at 7:57 AM, wrote:
> Date: Mon, 16 Apr 2018 06:28:52 -0400
> From: Alex
> To: gmx-us...@gromacs.org
> Subject: [gmx-users] gromos54a7 - topolbuild
> Message-ID:
>
> Content-Type: text/plain; charset="UTF-8"
>
> Dear all,
> I wonder if the topolbuild can provide the gromo
Quoting Justin Lemkul :
I just tested this in GROMACS 2018 and it works fine - if you provide
the protonated residue name, pdb2gmx correctly interprets the
protonation state. Do you have a use case that fails?
Is this behavior documented somewhere? I don't seem to find any mention of it.
My i
On 4/16/18 9:44 AM, mhuht...@abo.fi wrote:
Quoting Justin Lemkul :
I just tested this in GROMACS 2018 and it works fine - if you provide
the protonated residue name, pdb2gmx correctly interprets the
protonation state. Do you have a use case that fails?
Is this behavior documented somewhere?
Quoting Justin Lemkul :
problem. Please file a bug report on Redmine and include example input
files and pdb2gmx syntax you're using.
Ok, thanks. Bug posted at https://redmine.gromacs.org/issues/2480
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Dear all,
I am trying to perform free energy calculations of a small drug in octanol
using the GROMACS 5.1.3 software. I built a box of octanol using the
following command
gmx insert-molecules -ci oct.gro -nmol 125 -box 4 4 4 -o oct_box.gro
Followed by steepest descent minimization, 100 ps each of
Hi,
Make sure your particles have vdw on before you add charge to them. That's
usually the cause of this problem.
Mark
On Mon, Apr 16, 2018, 20:51 faride badalkhani
wrote:
> Dear all,
> I am trying to perform free energy calculations of a small drug in octanol
> using the GROMACS 5.1.3 softwa
Changing these parameters is not good, you may need to refer the forcefield
original articles.
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Refer this
http://manual.gromacs.org/documentation/5.1/user-guide/mdrun-performance.html
I use -ntmpi and -ntomp combination with -gpu_id
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Hello,
Thank you for the quick reply @ Mark Abraham. I am describing in detail
what i want to do. I have taken SWCNT (12*12)and encapsulate the molecule.
Now i want to check its binding free energy. I checked reference manual to
arrange the right order but didn’t success. can anyone have any other
Dear all,
I am trying to do REMD simulation in different cosolvents. I have generated
temperatures using temperature genrating tools but it gives different
number of temperatures in different solvents with exchange probability of
0.25. Is it fair to do remd with different replicas? In what way it w
Hi,
On Mon, Apr 16, 2018 at 10:21 AM ISHRAT JAHAN wrote:
> Dear all,
> I am trying to do REMD simulation in different cosolvents. I have generated
> temperatures using temperature genrating tools but it gives different
> number of temperatures in different solvents with exchange probability of
>
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