Zhang Bing,
I guess it is problem in your visualizers. Try to label the atom using VMD
which goes well with most of the file types derived in GROMACS. I hope
you'll see the atom as FE not just F.
Thanks
Peterson
--
View this message in context:
http://gromacs.5086.n6.nabble.com/Fwd-HEME-cystein
What do you mean? Am I supposed to use CGenFF to derive parameters?
Cheers,
Shima
From: Peter C. Lai
To: Discussion list for GROMACS users
Sent: Wednesday, May 9, 2012 5:20 AM
Subject: Re: [gmx-users] Formyl parameters
Where does swissparam get its parame
Dear Justin,
Thank you very much from your response.
Best Regards
Dina
From: Justin A. Lemkul
To: dina dusti ; Discussion list for GROMACS users
Sent: Wednesday, May 9, 2012 4:52 AM
Subject: Re: [gmx-users] radius of gyration
On 5/8/12 4:50 PM, dina du
you have position restraints on, which I expect would damp collisions between
solvent and solute. temp drops towards some sort of equilibrium, which doesn't
necessarily match your starting temp even though energy of the system is
conserved ..sounds like expected behavior to me?
--
Sent from my
Dear Gromacs experts,
I'm just a newbaby in Gromacs, and hence I have a lot of problem
when running this program. I try to run NVE simulation of a
protein. First, I run an NTP ensemble, follow by NVT and finally,
NVE. In NPT and NVT, T remains as constant, however, in NVE
simulation,
Where does swissparam get its parameters for charmm? and does it use custom
atomtypes for generic molecules? I have been using CGenFF-derived parameters
for molecules that aren't in base c36 and I think it's working well for me...
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Sent from my Android phone with K-9 Mail. Please excuse my bre
On 5/8/12 4:50 PM, dina dusti wrote:
Dear Justin,
Thank you very much from your help, but may I ask you to say me why the error
estimate of Rg is very smaller than Rgx, Rgy, Rgz, Please? I didn't understand
any thing from paper about this problem!
The value of Rg is calculated from the (x,y
Dear Justin,
Thank you very much from your help, but may I ask you to say me why the error
estimate of Rg is very smaller than Rgx, Rgy, Rgz, Please? I didn't understand
any thing from paper about this problem!
Best Regards
Dina
From: Justin A. Lemkul
To: d
On 5/8/12 4:08 PM, dina dusti wrote:
Dear Justin,
Thank you very much from your help.
Yes, the micelle was created after 100 ns from start of simulation.
If the first procedure is true, so why the error estimate is so small and why
the error estimate of Rg is so different with Rg(x,y,z)?
Fo
Dear Justin,
Thank you very much from your help.
Yes, the micelle was created after 100 ns from start of simulation.
If the first procedure is true, so why the error estimate is so small and why
the error estimate of Rg is so different with Rg(x,y,z)?
Please help me.
Best Regards
Dina
--
gmx-us
Hello community,
I recently ran several simulations using the g_bar method on several
molecule decouplings and I even applied it to some functional group
mutations and it seems to work out quite well so far. The only thing
is that it requires several simulations to run. I'm attempting to
replica
Hi Guys
I was using the program http://q4md-forcefieldtools.org/RED/ to derrive ESP
based charges for some molecules that I study using OPLSAA force field. Is this
a correct method to do so if not please let me know what are the other
methods that are available.
thanks alot
Milinda Samarawee
Hi Guys
I was using the program http://q4md-forcefieldtools.org/RED/ to derrive ESP
based charges for some molecules that I study. Is this a correct method to do
so if not please let me know what are the other methods that are available.
thanks alot
Milinda Samaraweera
University of Connecti
Dear Justin
I really appreciate for your reply.
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On 5/8/12 1:44 PM, ramesh cheerla wrote:
Dear Gromacs users,
I am planing to use wildcard atomtypes in [
dihedrals ] directive of the ffbonded.itp file, As my system contain O-C
dihedral, all the O-C dihedrals are same, so instead of mentioning each
dihedral exp
Dear Gromacs users,
I am planing to use wildcard atomtypes in [
dihedrals ] directive of the ffbonded.itp file, As my system contain O-C
dihedral, all the O-C dihedrals are same, so instead of mentioning each
dihedral explicitly i have tried wildcard atom types by
On 5/8/12 1:06 PM, dina dusti wrote:
Dear GROMACS Specialists,
I have one question about radius of gyration for micelle, Please help me.
My micelle is created at 10 ps by Martini CG force field.
Does this mean that during the first 100 ns, there is no micelle? That is, it
is only compl
Dear GROMACS Specialists,
I have one question about radius of gyration for micelle, Please help me.
My micelle is created at 10 ps by Martini CG force field.
When I calculate the radius of gyration from this time as "g_gyrate -f 1.xtc -s
1.tpr -n 1.ndx -o gyrate.xvg -b 10" and "g_analyze
On 5/8/12 11:40 AM, Za Pour wrote:
Dear gmx users
I am simulating a system involving carbon nanotube.
I successfully completed the EM,NVT and NPT equilibration phase and then
started to run production simulation(NVT ensemble) for 10 ns.However,
after passing more than 50 steps(1 ns),I gave
Dear gmx users
I am simulating a system involving carbon nanotube.
I successfully completed the EM,NVT and NPT equilibration phase and then
started to run production simulation(NVT ensemble) for 10 ns.However,
after passing more than 50 steps(1 ns),I gave the segmentation error.I
investigated
On 5/8/12 11:25 AM, Shima Arasteh wrote:
Dear gmx users,
My .pdb input file has a formyl group which is not defined in CHARMM27 and
CHARMM36. So I got its .itp file through swissparam. Now I want to use its
parametrs. As I read in gromacs.org , I need to include this .itp in .top file.
How doe
Dear gmx users,
My .pdb input file has a formyl group which is not defined in CHARMM27 and
CHARMM36. So I got its .itp file through swissparam. Now I want to use its
parametrs. As I read in gromacs.org , I need to include this .itp in .top
file. How does it come when I have not got any .top f
Hello,
I assume that you mean pull_pbcatom0...
Nothing changes when I set this to an atom index I am afraid.
I saw that you had use pull_geometry=cylinder in your recent JACS paper.
Would it be too much to ask to see those pull settings?
I simply cannot get the molecule to stay at the desired z-po
On 5/8/12 8:06 AM, rama david wrote:
Hi gromac friends
I am performing the justin tutorials on lipids
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials
I am strugling now on 3rd steps
I have following queris regarding to steps ...
1. I increase the van der walls radii of
Hi gromac friends
I am performing the justin tutorials on lipids
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials
I am strugling now on 3rd steps
I have following queris regarding to steps ...
1. I increase the van der walls radii of carbon from the 0.15 to 0.375
> Is t
Hi,
it is the ionic current, given by a sum over the center of mass
velocities of each molecule by their net-charge.
/Flo
On Mon, 2012-05-07 at 13:00 -0400, Andrew DeYoung wrote:
> Hi,
>
> g_current calculates the (ionic) current in the output file specified by the
> -o switch (by default, "c
On Tue, May 8, 2012 at 1:01 PM, rama david wrote:
>
>
> On Tue, May 8, 2012 at 1:00 PM, rama david wrote:
>
>> Hi Gromacs user,
>> I am doing the justin tutorial on lipid posted on link..
>>
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html
>>
>
g_density
8 maj 2012 kl. 03.29 skrev cuong nguyen:
> Dear,
>
> Could anyone please let me know, in Gromacs analysis is there any way to get
> the local pressure (along z-axis of the box)?
>
> Thanks a lot!
>
> Cuong Nguyen
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://li
On Tue, May 8, 2012 at 1:00 PM, rama david wrote:
> Hi Gromacs user,
> I am doing the justin tutorial on lipid posted on link..
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html
>
> I am following the tutorial very carefully ...
> As mentioned
That's the one.
7 maj 2012 kl. 22.34 skrev Christopher Neale:
> Dear users:
>
> I am writing my methods section for a simulation in which I used -vsites
> hydrogens and I want to ensure that I have the reference correct. The
> gmx-4.5.4 manual does not list a reference that I could see for thi
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