Hi Akash,
a cheap trick you can try (depending on your system) is to center your
trajectory on some residue or atom in the middle of your
protein/assembly/...
Otherwise it sometimes helps to invoke trjconv multiple times. First
with e.g. -pbc whole, and a second time with -center.
Peter
On 2
Hello Akash,
Let's assume that in your "non_water.tpr" group 1 is your protein; the
following always worked for me:
1 1 1 | gmx trjconv -f Nonwater.xtc -s non_water.tpr -pbc cluster - center
-boxcenter tric
of course "-boxcenter tric" depends on your box type
Sandor
On 21-11-17 21:54, Pandy
Dear gromacs users,
I'm trying to make a radial density profile function (NOT an rdf) from the
center of my vesicle. I'm trying to use the following command:
gmx density -f vesicle.gro -o density.xvg -s vesicle.tpr -center
I want it to make a radial density profile from the center of mass of the
Dear Gromacs,
After running
echo r 66 q|gmx make_ndx -f md_0_1.tpr -o index.ndx
I got the index.ndx file. However, all the sections are those default ones,
without the 66th residue atoms I want:
[ System ]
[ Protein ]
[ Protein-H ]
..
[ Ion ]
[ NA ]
[ CL ]
[ Water_and_ions ]
May I ask h
Hİ all,
I ran simulation of pvdf(ligand) in solution. My problem is pressure
fluctuation, My system's pressure fluctuated around reference pressure and
average pressure is not equal to my reference pressure. I did well
minimisation and nvt run for system before npt run. What should i do about
ave
Hi,
It's hard to say anything in the absence of any numbers about average or
fluctuations. Do check out
http://www.gromacs.org/Documentation/Terminology/Pressure
Mark
On Wed, Nov 22, 2017 at 9:59 PM ali akgün wrote:
> Hİ all,
>
> I ran simulation of pvdf(ligand) in solution. My problem is pre
Hİ,
Thank you for reply but can i minimize fluctuation?
On Wed, Nov 22, 2017 at 11:05 PM, Mark Abraham
wrote:
> Hi,
>
> It's hard to say anything in the absence of any numbers about average or
> fluctuations. Do check out
> http://www.gromacs.org/Documentation/Terminology/Pressure
>
> Mark
>
>
Dear Amber users
My protein system consist of two subunit chains alpha and beta each chain
consist four domains. I predicted the structure of both subunit chains now
i want to combine both structure subunits models, How i can combine them
in one pdb file. so that i can run the simulation on comp
Yes, by running longer, or on a larger system, just as statistical
mechanics predicts.
Mark
On Wed, Nov 22, 2017 at 10:16 PM ali akgün wrote:
> Hİ,
> Thank you for reply but can i minimize fluctuation?
>
> On Wed, Nov 22, 2017 at 11:05 PM, Mark Abraham
> wrote:
>
> > Hi,
> >
> > It's hard to
I will run with bigger nsteps (like monte carlo :D) , thank you for reply
sir.
On Wed, Nov 22, 2017 at 11:17 PM, Mark Abraham
wrote:
> Yes, by running longer, or on a larger system, just as statistical
> mechanics predicts.
>
> Mark
>
> On Wed, Nov 22, 2017 at 10:16 PM ali akgün
> wrote:
>
> >
Hi gromacs folks,
I was trying to introduce sulfenic acid as modified cysteine to the
forcefield as following. Everything went well until the "gmx mdrun -v
-deffnm em". The only file I modified was merged.rtp since there were no
new bond or dihedral angles. However my sulfenic acid falls apart (o
On 11/22/17 9:32 PM, MD wrote:
Hi gromacs folks,
I was trying to introduce sulfenic acid as modified cysteine to the
forcefield as following. Everything went well until the "gmx mdrun -v
-deffnm em". The only file I modified was merged.rtp since there were no
new bond or dihedral angles. Howe
Thanks Justin. Then do I need to create new bond of SG and OE in
ffbonded.itp? Cause I have tried adding SG and OE bond in ffbonded.itp and
I got complaint from gromacs.. I modified the SG-OE bond from S-O bond and
it should work...
On Wed, Nov 22, 2017 at 9:42 PM, Justin Lemkul wrote:
>
>
> On
On 11/22/17 9:57 PM, MD wrote:
Thanks Justin. Then do I need to create new bond of SG and OE in
ffbonded.itp? Cause I have tried adding SG and OE bond in ffbonded.itp and
SG and OE are atom names, not types. That's not a valid approach.
I got complaint from gromacs.. I modified the SG-OE b
Justin, originally I did use SG and OE in the [bonds] and I got
complaints of "SG-OE no default bond type" "CB SG OE" no default U-B type
and "CT1, CT2, SG, OE" no default proper dihedral gypes. Are these the
parameters you mean that are missing? If so, what files do you think I
should modify to
On 11/22/17 10:11 PM, MD wrote:
Justin, originally I did use SG and OE in the [bonds] and I got
complaints of "SG-OE no default bond type" "CB SG OE" no default U-B type
and "CT1, CT2, SG, OE" no default proper dihedral gypes. Are these the
Make sure you're clear on what needs to be done, b
Yes. You are right about the names. I wrote them by memory and they were
not printed from the terminal. I will try to edit the ffbonded.itp and see
how it goes. Thanks!
Ming
On Wed, Nov 22, 2017 at 10:14 PM, Justin Lemkul wrote:
>
>
> On 11/22/17 10:11 PM, MD wrote:
>
>> Justin, originally I di
Hi,
You need to specify each bond you want, and for the types of those bonds to
have parameters available. Bonds are specified with atoms, bond types are
specified with atom types.
Mark
On Thu, 23 Nov 2017 04:22 MD wrote:
> Yes. You are right about the names. I wrote them by memory and they we
Hello Sir,
I have run a simulation of amino-acid (glycine) with water molecules for 10
ns. Now i need to find out/analyze that whether the water molecules are
getting/more oriented towards N-terminal of glycine or towards the
C-terminal of glycine. (i hope this is what water orientation profile mea
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