You equilibrations are probably too short. There are some pretty slow
processes in lipid membranes.
Peter
On Fri, May 25, 2018 at 6:00 PM, Quyen V. Vu wrote:
> Hi Zeined,
> Have you check the energy , the box fluctuations and pressure deviations ?
> Best,
> Quyen
>
>
>
> On Fri, May 25, 2018 at
hain_B 1
> Protein_chain_B21
> Protein_chain_C 1
> Protein_chain_C21
> Protein_chain_D 1
> Protein_chain_D21
> LIG 1
> POT 118
> POPG96
> '''
>
> Insane script is for Martini, am I rig
Hi Alex,
Try either insane.py, or charmm-gui. I can't provide links, since I'm on my
phone.
You may need to generate the topology (itp) of the protein, which you can
do with calling pdb2gmx on just the protein. You should have a topology
(itp) of your favourite lipid.
Peter
On 18 Feb 2018 13:54
7;re very happy to make things work better!
>
> Mark
>
> On Mon, 6 Feb 2017 10:04 Kroon, P.C. wrote:
>
> > Alternatively, center it on an interfacial residue. pbc cluster doesn't
> > always work, unfortunately.
> >
> > Peter
> >
> >
Alternatively, center it on an interfacial residue. pbc cluster doesn't
always work, unfortunately.
Peter
On Sat, Feb 4, 2017 at 7:56 PM, Christopher Neale <
chris.ne...@alum.utoronto.ca> wrote:
> Awesome Mark, thanks! It works.
>
> I filed a bug about a nonexistent -clustercenter option mention
Hi,
yes it matters. In general tc-grps=system is better/correct, unless the
thermal energy transfer across your system is hampered (e.g. a lipid
membrane, or a large protein). It hasn't changed with versions. In
addition, the Berendsen thermostat produces the wrong ensemble.
To check previous simu
As an aside: Martini forcefield parameters are available in Gromacs format
on the Martini website. See
http://cgmartini.nl/index.php/force-field-parameters
Peter
On Thu, Jul 21, 2016 at 2:05 PM, Marlon Sidore
wrote:
> Thanks for your answer, that solved everything.
>
> Marlon
>
> Marlon Sidore
t; membrane (A) and one in the water (B) and simulate it independently 10
> times to collect statistics about associations of A and B during those
> runs. The problems that I don't know how to put 2 different unbound
> proteins in the MARTINI system.
>
> James
>
> 2016-04-18
Hi,
I assume you want to study the binding of your water soluble protein to
your membrane(protein). DAFT was created to do just this. DOI:
10.1021/ct5010092
Peter
On Fri, Apr 15, 2016 at 3:37 PM, James Starlight
wrote:
> Dear Gromacs users!
>
> I am looking for some tutorial for the MARTINI si
; >>
> >> that is waht related to constraints in my mdp
> >> constraints = none
> >> constraint_algorithm = Lincs
> >> unconstrained_start = no
> >> lincs_order = 2
> >> lincs_warnangle = 30
&g
light
wrote:
> an question: might the bigger -rdd like 1.8 or 2.0 produce ssmth bad
> in simulation? generally I found that with rdd 1.8 the siduation is
> better, also I reduced number of CPU for that job from 256 to 128 and
> it works OK by now!
>
> Gleb
>
> 2016-04
Hi James,
1) use a newer version of Gromacs
2) try passing -rdd 1.4 or even 1.6 to mdrun. The bonds in Elnedyn are so
long and flexible they occasionally confuse gromacs' domain decomposition.
Peter
On Thu, Apr 14, 2016 at 8:49 AM, James Starlight
wrote:
> Dear Gromacs Users!
>
> I faced with
This is a known bug in Martinize; you applied the correct fix.
And Justin is right, it would have been better to post this kind of
question on the Martini forum (www.cgmartini.nl); I'm also rather sure that
this answer is on there somewhere.
Peter
On Tue, Apr 12, 2016 at 8:43 PM, Justin Lemkul w
Just use your favourite text editor.
Peter
On Thu, Aug 20, 2015 at 3:10 AM, wrote:
> Line 52 of cmake/FindSphinx.cmake file is written below.
> string(REGEX REPLACE "Sphinx \\([^)]*\\) ([^ ]+)" "\\1"
> SPHINX_EXECUTABLE_VERSION "${SPHINX_VERSION_OUTPUT_VARIABLE}")
>
> Can you tell me how I can
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