On 2013-06-14 21:39, Jeffery Perkins wrote:
Your calculation seems correct. Which gmx version did you use?
The correlation between the numbers is almost 100% so there must be a
simple explanation.
gmx version is 4.5.4, and yeah the correlation is odd, in the code you
listed:
Then that is the
Hello, everyone,
I recently use g_chi to calculate the omega dihedrals of 17-residue
peptide. But the results are almost far away from 180 and -180 degree. The
omega dihedrals from the structure show 180 or -180 degree. Does the tool
have some bug? Moreover, g_chi only gave me 15 output files,
Hi GMX users!
Does anyone here have experience creating custom toplogies for the 53A6
forcefield?
I'm currently trying to 'bind' the Fe, of a heme, to a Cys residue to
simulate coordination. I've looked into using PRODRG2 and ATB servers,
however they do not support such generation
Any assistanc
Dear Justin,
Thanks a lot. I used this and it works fine:
editconf -f final.pdb -o final.gro -c -d 0.0
regards,
Jiomm
On Sat, Jun 15, 2013 at 3:09 AM, Justin Lemkul wrote:
>
>
> On 6/14/13 8:08 PM, gromacs query wrote:
>
>> Dear Justin,
>>
>> I saw your tutorial (
>> http://www.bevanlab.bioc
On 6/14/13 8:08 PM, gromacs query wrote:
Dear Justin,
I saw your tutorial (
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html
)
But my case is different. I can not even generate tpr file (trjconv as
tutorial says) as it need box info
Can
Dear Justin,
I saw your tutorial (
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html
)
But my case is different. I can not even generate tpr file (trjconv as
tutorial says) as it need box info
Can you please suggest what can be the best possi
I have a bizzar problem. I did 21 simulation for 4 ns each. These were equ'd for 4ns prior, then taken from an assembly run over 4ns so between 300 pico and 4ns additional each. A reviewer wants a couple extnded ends added,say like 4 extra ns, which I can only do 1-4 at most due to time limi
On 6/14/13 7:37 PM, gromacs query wrote:
Dear Justin,
Thanks for reply. Yes sorry indeed its taking box vector from pdb (which I
dont want to use as I think they are wrong). In my case if I have already
water molecules in my system then if I use:
editconf -f del.pdb -o del.gro -c -d 0.0 -bt c
Dear Justin,
Thanks for reply. Yes sorry indeed its taking box vector from pdb (which I
dont want to use as I think they are wrong). In my case if I have already
water molecules in my system then if I use:
editconf -f del.pdb -o del.gro -c -d 0.0 -bt cubic
even now also I see pbc box (in vmd) it
On 6/14/13 7:03 PM, Parker de Waal wrote:
Thanks Justin!
I've updated the values accordingly. However can I ask where you found
these? I'm curious if there is a site that I missed while searching.
Cutoff values are described in the primary literature for the force field of
interest.
-Jus
Thanks Justin!
I've updated the values accordingly. However can I ask where you found
these? I'm curious if there is a site that I missed while searching.
Best,
Parker
On Fri, Jun 14, 2013 at 12:04 PM, Justin Lemkul wrote:
>
>
> On 6/14/13 10:45 AM, Parker de Waal wrote:
> > HI Maggin,
> >
>
Hi,
I have run a 5 ns simulation with a small protein in water [SPCE]. I am
interested in the rate of breakage (sense of how quickly / slowly hbonds are
broken and formed) of hbonds between protein and solvent. I ran g_hbond -ac
for the trajectory and received the following output:
Normalization
On 6/14/13 4:58 PM, gromacs query wrote:
Dear All,
I have two different membrane systems (membrane with waters only) already
with me. So I dont need to add solvent molecules.
So to start with simulation I need box size (last line in gro file). I used
following command (for both cases):
editc
Dear All,
I have two different membrane systems (membrane with waters only) already
with me. So I dont need to add solvent molecules.
So to start with simulation I need box size (last line in gro file). I used
following command (for both cases):
editconf -f del.pdb -o del.gro -c -bt cubic
Firs
>Your calculation seems correct. Which gmx version did you use?
>The correlation between the numbers is almost 100% so there must be a
>simple explanation.
gmx version is 4.5.4, and yeah the correlation is odd, in the code you
listed:
>> pv = vol*md->ref_p/PRESFAC;
>>
>>
On 2013-06-14 19:28, Jeffery Perkins wrote:
or should i be doing < U+*ref_p > = ?
More specifically, + *ref_p = H
isn't really meaningful thing. I mean, you can define something
such that = H, but that's not really thermodynamics.
sorry I always have issues deciding how to talk about
Dear all,
I am trying to perform all-atom simulations of a protein+lipid system with
charmm27 forcefield in gromacs . Can anyone suggest me from where I could
obtain the paramaters( *.itp file) from? I tried searching the lipid-book but
in vain.cGENFF and swissparam are exclusively for small mo
or should i be doing < U+*ref_p > = ?
>>
>>> More specifically, + *ref_p = H
>>
>>> isn't really meaningful thing. I mean, you can define something
>>> such that = H, but that's not really thermodynamics.
>>
>> sorry I always have issues deciding how to talk about this stuff, so
>>
Hi Mark,
Sorry for my carelessness. I check my email again and see your reply. I get
your point that my problem may be (at least part of) caused by RNG of the
thermostat.
Thanks again and sorry for my careless bothering.
Cheers,
Cuiying
> On Fri, Jun 14, 2013 at 12:52 AM, Cuiying Jia
On 6/14/13 10:45 AM, Parker de Waal wrote:
HI Maggin,
The Pressure came from NPT simulation, I apologize for the lack of
annotation. Here are some of the outputs of your suggested checks of
equilibrium
https://docs.google.com/spreadsheet/ccc?key=0Ao2bINpUakZ-dHpiZG9SOXhkX0JGNXlqTHBfQ1kwbnc&usp
On 6/14/13 7:22 AM, maggin wrote:
Hi, Justin,
If I use Pymol to set up a mutation of 1dx0.pdb, If it best do Steepest
Descents in vacuo first ?
I have no idea. There are many ways you can probably dream up to proceed with
any system. For normal proteins in water, I never waste time with
On 6/14/13 6:35 AM, Jianguo Li wrote:
You can try move "md.log" to some folder and then copy back such as:
1) mv md.log /some_folder
2) cp /some_folder/md.log .
Otherwise use -noappend in the mdrun command. All the important files can be
concatenated after the run, anyway.
-Justin
-
On 6/14/13 6:33 AM, maggin wrote:
Hi, Justin,
At md step, protein run out of box, if it will better that set position
constraint, let protein at center of box?
There is no such thing as "outside" of an infinite system using periodic
boundary conditions.
http://www.gromacs.org/Documentatio
HI Maggin,
The Pressure came from NPT simulation, I apologize for the lack of
annotation. Here are some of the outputs of your suggested checks of
equilibrium
https://docs.google.com/spreadsheet/ccc?key=0Ao2bINpUakZ-dHpiZG9SOXhkX0JGNXlqTHBfQ1kwbnc&usp=sharing
I'm currently looking into the rvdw
Hi, Parker,
gromos53a6 force field, rvdw=1, if it right ? please check.
Your ref_p = 1.0, So, Pressure average of 1.9 is come from which step? NVT,
NPT, md ?
Actually, we use: g_energy -f npt.edr -o pressure.xvg
to see if NPT has reached equilibrium.
g_energy -f nvt.edr
to see if NVT has
I appreciate you for your useful guidance
I want to determine the minimum distances between COM (center of mass)
of a surfactant molecule and that of number of other surfactants but
g_mindist compute the distances between one group and a number of
other groups. It is not quite clear for me that g_
Hi Mark,
Thanks for your response,
Currently I'm using the gromos53a6 force field because it is compatible
with heme cofactor found within P450.
I'll look through the literature again to double check my settings for my
NvT, NpT and energy minimization steps
as well, however any further insight wo
Hi, Justin,
If I use Pymol to set up a mutation of 1dx0.pdb, If it best do Steepest
Descents in vacuo first ?
Thank you very much!
maggin
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Sent from the GROMACS Users Forum mai
On Wed, Jun 12, 2013 at 11:26 AM, C.M.Sampson wrote:
> Dear all,
>
> I'm using Gromacs 4.5.5 with the amber ff99SB forcefield to run NVE
> simulations on ethane in 725 TIP3P water molecules. I used antechamber
> to parametrise my ethane.
>
> I have 2 issues;
>
> Firstly the energy conservation o
Constraints make the job of the minimizer more difficult. If the starting
configuration is bad enough that the EM step might be really useful, give
the potential energy surface a free run without constraints. And then in
such cases do a preliminary NVT with dt=0.0005 and no constraints to get
thing
Hi, Justin,
Thank you very much for your help!
Another question is when we do steep minimization, if it will be better
first do steep with constraint, then do steep without constraint?
Thank you very much!
maggin
--
View this message in context:
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You can try move "md.log" to some folder and then copy back such as:
1) mv md.log /some_folder
2) cp /some_folder/md.log .
It works for me
Jianguo
- Original Message -
From: zhaowh
To: gmx-users ; gmx-users ;
gmx-users ; gmx-users ; gmx-users
; gmx-users
Cc:
Sent: Friday, 1
Hi, Justin,
At md step, protein run out of box, if it will better that set position
constraint, let protein at center of box?
Thank you very much!
maggin
--
View this message in context:
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Sent from the GROMACS U
Hi everyone,
When I restart the simulation as the following: "mdrun -s tpxout -cpi", a fatal
error is arised (Fatal error: Failed to lock: md.log. Already running
simulation?). But I have the files: md.log, traj.xtc, ender.edr, etc.
Thank you for your attention and answer.
zhaowh--
gmx-use
On 6/14/13 3:33 AM, maggin wrote:
Before do Steepest with water, we first do Steepest Descents in vacuo, if
such way will better to only do Steepest with water ?
Steepest descents is a fairly robust method, and as such, I rarely (if ever) do
in vacuo minimization before minimizing my who
On 6/14/13 2:58 AM, maggin wrote:
at md stage,
can we set refcoord_scaling = com as follows,
; Pressure coupling is on
pcoupl = Parrinello-Rahman; Pressure coupling on in NPT
pcoupltype = isotropic ; uniform scaling of box vectors
tau_p= 2.0 ; time constant, in ps
ref_p
Hi, Tsjerk,
Oh, so that's it . Thank you very much!
maggin
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gmx-users mailing listgmx-users@gromacs.org
On Thu, Jun 13, 2013 at 11:59 PM, Parker de Waal
wrote:
> Hi everyone,
>
> I recently tried to perform an 25 ns simulation on 12 nodes and was greeted
> with this error around 3.2 ns into the run.
>
> '3 particles communicated to PME node 9 are more than 2/3 times the cut-off
> out of the domain d
On Fri, Jun 14, 2013 at 12:52 AM, Cuiying Jian wrote:
> Hi GROMACS Users,
>
> I am sorry if you are bothered by my second post about this topic. But the
> fact is that I tested restarting simulations with .cpt files by GROMACS
> 4.6.1. and I still cannot get binary identical results from restarte
Hi Maggin,
The constraints are typically used during MD simulation to allow larger
time steps.
Cheers,
Tsjerk
On Fri, Jun 14, 2013 at 9:39 AM, maggin wrote:
> Hi, Tsjerk,
>
> I have one question that in what situation people do constraint ?
>
> Thank you very much!
>
> maggin
>
>
>
> --
> Vi
Hi, Tsjerk,
I have one question that in what situation people do constraint ?
Thank you very much!
maggin
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g
Before do Steepest with water, we first do Steepest Descents in vacuo, if
such way will better to only do Steepest with water ?
Thank you very much!
maggin
--
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Sent from the GROMACS U
at md stage,
can we set refcoord_scaling = com as follows,
; Pressure coupling is on
pcoupl = Parrinello-Rahman; Pressure coupling on in NPT
pcoupltype = isotropic ; uniform scaling of box vectors
tau_p= 2.0 ; time constant, in ps
ref_p= 1.0 ; reference pressure,
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