Can you send me the parameters I need to usefor FE
On Mon, Apr 16, 2012 at 2:55 PM, francesco oteri
wrote:
> Hi,
> You have to had LJ parameters in ffnonbonded.itp file in the subfolder
> relative to your force-field
>
> Francesco
>
> Il giorno 16 aprile 2012 11:08, Kamalesh Roy ha
> sc
Dear Shouliang,
Thanks. Maybe the developers can help undertand why GTX560 is not
included on the GPU compatibility list for GROMACS?
-G
2012/4/16 shouliang dong :
> It is compatible with GROMACS.
>
> 在 2012年4月14日 上午11:32，Gaurav Goel 写道：
>>
>> Dear All,
>>
>> Can you please guide me on how to fi
Mark,
According to the manual, the temperature of a group should always be
calculated from the total KE of the group (see eq 3.13 in the manual), which
presumably includes contributions from the translational motion of the
center of mass of the group, plus the rotational motion around the center
Andrew DeYoung wrote:
Hi,
What is the parameter epsilon_r mentioned in the manual
(http://manual.gromacs.org/current/online/mdp_opt.html#el)? The manual says
that it is the relative dielectric constant. My initial thought was that
this would only be relevant for reaction-field electrostatics
Hi,
What is the parameter epsilon_r mentioned in the manual
(http://manual.gromacs.org/current/online/mdp_opt.html#el)? The manual says
that it is the relative dielectric constant. My initial thought was that
this would only be relevant for reaction-field electrostatics, or somewhere
where impli
Andrew DeYoung wrote:
Hi,
Does the parameter ewald_rtol affect PME electrostatics (coulombtype = PME),
or does ewald_rtol only affect Ewald electrostatics (coulombtype = Ewald)?
In the manual description of the .mdp parameters
(http://manual.gromacs.org/current/online/mdp_opt.html#el), it says
Hi,
Does the parameter ewald_rtol affect PME electrostatics (coulombtype = PME),
or does ewald_rtol only affect Ewald electrostatics (coulombtype = Ewald)?
In the manual description of the .mdp parameters
(http://manual.gromacs.org/current/online/mdp_opt.html#el), it says in the
Ewald section, "Th
Shyno Mathew wrote:
Hey Justin,
thanks for your reply.
For gen_vel, the manual says "Generate velocities in grompp according to
a Maxwell distribution at temperature gen_temp [K], with random seed
gen_seed. This is only meaningful with integrator
md"
Since the integrator I am using is sd, I
Shima Arasteh wrote:
So, I can not use the coordinates of the output files of gromos runs. Right?
Not without significant modification of names, presence of H atoms, etc. You'll
need to regenerate a suitable topology, as has been said, and then run thorough
equilibration under the new forc
On 2012-04-16 10:14:01AM -0700, Shima Arasteh wrote:
> So, I can not use the coordinates of the output files of gromos runs. Right?
You can but you may need to rename the atoms for each residue for pdb2gmx
to work.
>
>
>
> From: Peter C. Lai
> To: Discussion l
Hey Justin,
thanks for your reply.
For gen_vel, the manual says "Generate velocities in grompp according to a
Maxwell distribution at temperature gen_temp [K], with random seed
gen_seed. This is only meaningful with integrator
md"
Since the integrator I am using is sd, I put 'gen_vel no'
Yes you a
So, I can not use the coordinates of the output files of gromos runs. Right?
From: Peter C. Lai
To: Discussion list for GROMACS users
Sent: Monday, April 16, 2012 8:23 PM
Subject: Re: [gmx-users] GROMOS87 and CHARMM27
On 2012-04-16 08:26:00AM -0700, Shima Ar
Shyno Mathew wrote:
Hello Prof. David,
thanks for your reply.
I will try using isotropic pressure scaling. But still I am not clear
why the simulations ran fine with first .mdp file. As mentioned in the
previous email only few parameters were different in my .mdp file
compared to my advisor
Hello Prof. David,
thanks for your reply.
I will try using isotropic pressure scaling. But still I am not clear why
the simulations ran fine with first .mdp file. As mentioned in the previous
email only few parameters were different in my .mdp file compared to my
advisor's.
I am just copying those
On Mon, Apr 16, 2012 at 11:01 PM, sai nitin wrote:
> Hi all,
>
> I have done complex (protein + ligand) complex from autodock software using
> this complex im trying to follow
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/01_pdb2gmx.html
> tutorial
>
> But when
On 17/04/2012 1:50 AM, Laura Leay wrote:
On Fri, 2012-04-13 at 11:01 +1000, Mark Abraham wrote:
On 13/04/2012 2:48 AM, Laura Leay wrote:
All,
I'm trying to run a tabulated soft core potential with the form V =
A + Br^2 + Cr^3 up to about r=0.1 A and the normal LJ 6-12 potential
after this.
I'
On 2012-04-16 08:26:00AM -0700, Shima Arasteh wrote:
> Dear GROMACS users,
>
> I reproduced the results of a protein-membrane system by using force field
> GROMOSE87. This protein forms ion channel in membrane.
> Now if I wanna study the ion conduction through this channel using force
> field CH
On Fri, 2012-04-13 at 11:01 +1000, Mark Abraham wrote:
> On 13/04/2012 2:48 AM, Laura Leay wrote:
> > All,
> >
> > I'm trying to run a tabulated soft core potential with the form V =
> > A + Br^2 + Cr^3 up to about r=0.1 A and the normal LJ 6-12 potential
> > after this.
> >
> > I've chosen the
On 2012-04-16 17:23, Shyno Mathew wrote:
Dear Gromcas users,
I am doing some mutation study, NPT simulations. Initially I was using a
generic .mdp file I got from my advisor and I was able to run the
systems for ~50ns with out any issues.
But then I spend time reading about gromacs and created a
Dear GROMACS users,
I reproduced the results of a protein-membrane system by using force field
GROMOSE87. This protein forms ion channel in membrane.
Now if I wanna study the ion conduction through this channel using force field
CHARMM27 in umbrella sampling method, is it possible? Can I use the
Dear Gromcas users,
I am doing some mutation study, NPT simulations. Initially I was using a
generic .mdp file I got from my advisor and I was able to run the systems
for ~50ns with out any issues.
But then I spend time reading about gromacs and created a .mdp file.
However, with my .mdp file the r
An easy way to build a protein in a bilayer is through the charmm-gui
website
www.charmm-gui.org/
Partial drawbacks are that you need CHARMM to perform final equilibration
and then may need to rename some atoms to work with GROMACS
On plus side is that charmm36.ff retains the original CHARMM atom
On 17/04/2012 1:14 AM, Sanku M wrote:
Hi,
Is there any known issue/problem in running FEP calculations with
charm27.ff in gromacs4.5.4 ? I tried running an FEP calculation using
charmm27.ff by interpolating A state and B state but it gives error
that dihedral terms with multiple values can no
Hi,
Is there any known issue/problem in running FEP calculations with charm27.ff
in gromacs4.5.4 ? I tried running an FEP calculation using charmm27.ff by
interpolating A state and B state but it gives error that dihedral terms with
multiple values can not be interpolated..One need to write all
sai nitin wrote:
Hi all,
I have done complex (protein + ligand) complex from autodock software
using this complex im trying to follow
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/01_pdb2gmx.html
tutorial
But when i take complex structure directly from a
Hi all,
I have done complex (protein + ligand) complex from autodock software using
this complex im trying to follow
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/01_pdb2gmx.html
tutorial
But when i take complex structure directly from autodock result and run
PDB
16 apr 2012 kl. 13.32 skrev Justin A. Lemkul:
>
>
> 李 麗花 wrote:
>> Hi:
>> I am getting upsep to install DSSP in linux with Gromacs 4.0.7
>> I do not know where is the problem
>> which DSSP file I should download it
>> and possible because gromacs 4.0.7 ?
>> could someone can help me to figure o
Thankl you.
Well... Indeed, just removed them manually and everything is ok.
Steven
On Mon, Apr 16, 2012 at 2:38 PM, Peter C. Lai wrote:
> Sounds like a bad VMD selection that didn't remove MNZ1 when you did the
> conversion. MNZ1 sounds like a virtual site for the extra hydrogen off NZ
> in pr
James Starlight wrote:
Justin,
Thank you for explanation. Tomorrow I'll try to check results of
simulation with the disres applied with its default values as well as
with narrower -disre_dist values ( ignorring -disre_frac option at all
) and post here results of such simulations.
1) T
Justin,
Thank you for explanation. Tomorrow I'll try to check results of simulation
with the disres applied with its default values as well as with narrower
-disre_dist values ( ignorring -disre_frac option at all ) and post here
results of such simulations.
1) The cut-off distance wich I've s
Sounds like a bad VMD selection that didn't remove MNZ1 when you did the
conversion. MNZ1 sounds like a virtual site for the extra hydrogen off NZ
in protonated LYS.
On 2012-04-16 02:32:09PM +0100, Steven Neumann wrote:
> Dear Gmx Users,
>
> I run implicit simulation for 1 us with virtual sites o
James Starlight wrote:
Justin,
I've applied disres on each backbone atom of my potein within cutoff
distance of 1nm ( Rc=1.0 nm). I've selected this value for cutoff to
decrease overall ammount of the restains in my itp file. Also such value
( 1nm) was selected because of the relatively ti
Dear all,
Im using wham on series of runs and have run into the following proble.
The command line
>g_wham_d -if pullf.dat -it tpr.dat -temp 300 -o whamf.xvg -hist outf.hist
>-unit kCal
will work in one run, but not the next one as I go through I found a couple
that give the error
Fatal er
Dear Gmx Users,
I run implicit simulation for 1 us with virtual sites on hydrogens, then
using VMD extracted coordinates into the pdb file. As I want to run
explicit solvent simulation now I removed hydrogens so that pdb2gmx will
add them. Then I got an error while trying to pdb2gmx using Charmm27
Justin,
I've applied disres on each backbone atom of my potein within cutoff
distance of 1nm ( Rc=1.0 nm). I've selected this value for cutoff to
decrease overall ammount of the restains in my itp file. Also such value (
1nm) was selected because of the relatively tight packing of the alpha
helic
On 16/04/2012 8:43 PM, Gavin Melaugh wrote:
Hi all
What does the following note mean in the log file
DD load balancing is limited by minimum cell size in dimension Z
Is is purely a performance related issue ?
Yes. See 3.17.2 for description of DLB. Various algorithms constrain
minimum cell
Hi Erik,
Thank you very much from your response.
Best Regards
Dina
From: Erik Marklund
To: dina dusti ; Discussion list for GROMACS users
Sent: Monday, April 16, 2012 12:07 PM
Subject: Re: [gmx-users] Clustering
Hi,
It's been a while since I used g_clu
李 麗花 wrote:
Hi:
I am getting upsep to install DSSP in linux with Gromacs 4.0.7
I do not know where is the problem
which DSSP file I should download it
and possible because gromacs 4.0.7 ?
could someone can help me to figure out it ?
many thanks
http://swift.cmbi.ru.nl/gv/dssp/
Under "Misce
Hi:I am getting upsep to install DSSP in linux with Gromacs 4.0.7I do not know
where is the problemwhich DSSP file I should download itand possible because
gromacs 4.0.7 ?could someone can help me to figure out it ?many thanks
Best Wishesli-hua --
gmx-us
James Starlight wrote:
Dear Gromacs Users!
By that moments I've completed 2 sets of simulation in high temperature
1- With applied posres on the backbone atoms ( fc= 200 ).
The result was- that the posres prevented motion of the helixes as the
rigid bodies so I've not noticed any conformati
Hi all
What does the following note mean in the log file
DD load balancing is limited by minimum cell size in dimension Z
Is is purely a performance related issue ?
Cheers
Gavin
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please sear
Hi,
You have to had LJ parameters in ffnonbonded.itp file in the subfolder
relative to your force-field
Francesco
Il giorno 16 aprile 2012 11:08, Kamalesh Roy ha
scritto:
> CAn any one siggest me how can I run simulation a protein containing Fe
> atom,
> I have changed the iions.itpfile and inc
CAn any one siggest me how can I run simulation a protein containing Fe
atom,
I have changed the iions.itpfile and included there Fe in residue type.dat
bu still it is returning an error.
FE parameter not found.
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/l
Dear All,
Is there a way to extract the pull force (and not the total force or energy)
for a specified group (indexed) or center of mass, rather than just the total
pullf over a run? I wanted to break up the pullf into varied sub
contributions, however as it is applied to the center of mass o
Hi,
It's been a while since I used g_clustsize, but if I'm not mistaken you get the
number of molecules per cluster as output, from which you can estimate the
physical size of the clusters with a few assumptions. If that's not good enough
you also get the identities of the molecules in the clus
Dear Gromacs Users!
By that moments I've completed 2 sets of simulation in high temperature
1- With applied posres on the backbone atoms ( fc= 200 ).
The result was- that the posres prevented motion of the helixes as the
rigid bodies so I've not noticed any conformation sampling.
Question : Cou
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