>
> On 2/12/13 1:12 AM, neeru sharma wrote:
> > Dear Gromacs Users,
> >
> >
> > I have simulated a system of protein-ion complex. As a part of the
> > analysis, I want to see whether there are any H-bonds or other
> interactions
> > between the active site residues and the water surrounding those
>
hi all,
i am trying to find the coordination number using the rdf between two chains
in the system .my box contains two polymer chains with water molecules.i know
integrating 4*pi*r*r*g(r)*rho between 0 to first minima of rdf will give
coordination number .the first minima value i took from the rdf
Thanks for your answer Justin. I followed your advice:
When I type
*$ source /usr/local/gromacs/bin/GMXRC*
*$*
Nothing happened, the prompt returns normally and no action is executed. Do
you have any idea?
On Tue, Feb 12, 2013 at 11:27 PM, Justin Lemkul wrote:
>
>
> On 2/12/13 9:24 PM, David S
Hi,
I am sorry if this topic is not relevant for GROMACS forum, but I hope
someone has faced the same problem before and could give me some advice...
I need to simulate a relatively short protein (170aa) in water. No
structures are available for it, so I used a Modeller web server to get
some. Un
On 2/12/13 9:24 PM, David Sáez wrote:
Hello everybody, I'm trying to install Gromacs 4.6 in my Ubuntu 12.04
laptop. As I am not a a skilled user, I tried the Quick and Dirty
Installation, After following the instructions I obtained this message when
trying to execute GMXRC:
david@HAL-9000:~$ /
Hello everybody, I'm trying to install Gromacs 4.6 in my Ubuntu 12.04
laptop. As I am not a a skilled user, I tried the Quick and Dirty
Installation, After following the instructions I obtained this message when
trying to execute GMXRC:
david@HAL-9000:~$ /usr/local/gromacs/bin/GMXRC
/usr/local/gro
On 2/12/13 5:44 PM, Sonia Aguilera wrote:
Thank you Justin,
So, your advice is not to perform the npt calculation and to run the md
after the nvt?
A common mistake is to think that there is a "standard" protocol that one must
follow. While it is true that for the condensed phase, a common
Thank you Justin,
So, your advice is not to perform the npt calculation and to run the md
after the nvt?
Thank you,
Sonia Aguilera
--
View this message in context:
http://gromacs.5086.n6.nabble.com/Error-The-Y-size-of-the-box-times-the-triclinic-skew-factor-is-smaller-than-the-number-of-DD
On 2/12/13 5:24 PM, Sonia Aguilera wrote:
Hi,
I was performing a NPT calculation, and I got this error:
The Y-size of the box (6.002812) times the triclinic skew factor (1.00)
is smaller than the number of DD cells (6) times the smallest allowed cell
size (1.000605)
I also tried to chang
Hi,
I was performing a NPT calculation, and I got this error:
The Y-size of the box (6.002812) times the triclinic skew factor (1.00)
is smaller than the number of DD cells (6) times the smallest allowed cell
size (1.000605)
I also tried to change the number of processors but I got the same
On 2/12/13 10:29 AM, vidhya sankar wrote:
Dear Justin Thank you for your reply,
I have set the Restraint Along the Z Axis . as follows
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
i funct fcxfcyfcz
1
On 2/12/13 9:57 AM, Steven Neumann wrote:
On Tue, Feb 12, 2013 at 2:53 PM, Justin Lemkul wrote:
On 2/12/13 9:40 AM, Steven Neumann wrote:
Dear Gmx Users,
I know it is possible to combine windows with different spring
constants into the one PMF curve using g_wham.
Do I have to somehow te
On 2/12/13 11:06 AM, escajarro wrote:
Hello all,
I am afraid that, after reading all the documentation I could find about
Coul-SR and LJ-SR, I still do not understand what these terms account for.
I am running a simulation of one single polymer chain in water. My values
for cut-off radious ar
On 2/12/13 11:29 AM, Kavyashree M wrote:
Dear Users,
How can intra-protein hydrophobic contacts be found
for a trajectory. Most of the mails regarding this in the
list is regarding hydrophobic contacts between chains
or ligand and protein. So kindly help.
Create a group of hydrophobic atoms
Hello all,
I am afraid that, after reading all the documentation I could find about
Coul-SR and LJ-SR, I still do not understand what these terms account for.
I am running a simulation of one single polymer chain in water. My values
for cut-off radious are rlist=rcoulomb=rvdw=1.5, I am using PME
Dear Justin Thank you for your reply,
I have set the Restraint Along the Z Axis . as follows
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
i funct fcx fcy fcz
1 1 0 0 100
#endif
A
On Tue, Feb 12, 2013 at 2:53 PM, Justin Lemkul wrote:
>
>
> On 2/12/13 9:40 AM, Steven Neumann wrote:
>>
>> Dear Gmx Users,
>>
>> I know it is possible to combine windows with different spring
>> constants into the one PMF curve using g_wham.
>>
>> Do I have to somehow tell g_wham that one or two
On 2/12/13 9:40 AM, Steven Neumann wrote:
Dear Gmx Users,
I know it is possible to combine windows with different spring
constants into the one PMF curve using g_wham.
Do I have to somehow tell g_wham that one or two windows have
different spring constants?
No, they are read from the .tpr
On 2/12/13 9:45 AM, Albert wrote:
Hello:
I've got a question for setting of .mdp file for MD productions. The .trr file
is really huge if we are going to run longer MD simulations. In this case, I
usually only consider generate .xtc file, but the velocity is missed for all
steps except the l
Hello:
I've got a question for setting of .mdp file for MD productions. The
.trr file is really huge if we are going to run longer MD simulations.
In this case, I usually only consider generate .xtc file, but the
velocity is missed for all steps except the last one.
So I am just wondering,
On 02/12/2013 03:33 PM, Justin Lemkul wrote:
gmxcheck is your friend, as well as the wiki.
http://www.gromacs.org/Documentation/File_Formats/Checkpoint_File
A checkpoint file is always written at the last step of the
simulation, which seems to be what you were asking for previously.
-Just
On 2/12/13 9:32 AM, Albert wrote:
On 02/12/2013 03:28 PM, Justin Lemkul wrote:
Extract it from the .cpt file that corresponds to that frame.
-Justin
thanks a lot for such helpful comments. I found that the md production produced
two .cpt file:
state.cpt
state_prev.cpt
I am not sure whic
On 02/12/2013 03:28 PM, Justin Lemkul wrote:
Extract it from the .cpt file that corresponds to that frame.
-Justin
thanks a lot for such helpful comments. I found that the md production
produced two .cpt file:
state.cpt
state_prev.cpt
I am not sure which one would be the one I need D
On 2/12/13 9:25 AM, Albert wrote:
On 02/12/2013 03:19 PM, Justin Lemkul wrote:
Velocities are not stored in .xtc files. They are stored in .trr files, if
nstvout != 0 in the .mdp file.
-Justin
Hi Justin:
thanks for kind comments. I used the following settings and I didn't generate
.trr
On 02/12/2013 03:19 PM, Justin Lemkul wrote:
Velocities are not stored in .xtc files. They are stored in .trr
files, if nstvout != 0 in the .mdp file.
-Justin
Hi Justin:
thanks for kind comments. I used the following settings and I didn't
generate .trr file:
nstxout= 0
On 2/12/13 9:17 AM, Albert wrote:
Hello:
I am using Gromacs4.6 and I extract one of my frame into .gro file by command:
trjconv_mpi -f md.xtc -s md.tpr -dump 25000 -o md.gro
I found that the velocity information was not present in this 25ns-md.gro file:
Velocities are not stored in .xtc
Hello:
I am using Gromacs4.6 and I extract one of my frame into .gro file by
command:
trjconv_mpi -f md.xtc -s md.tpr -dump 25000 -o md.gro
I found that the velocity information was not present in this
25ns-md.gro file:
Generated by trjconv : Protein t= 25000.0
54178
1TYR N
On 2/12/13 8:37 AM, durdagis wrote:
Justin, it's not the artifacts of visualization program. At the beginning
distance for isopeptide bond is 1.38 Angs (and it's defined at the
specbond.dat);
LYS NZ 1 GLY C 1 0.13LYQ GLQ
together with energy minimization thi
Justin, it's not the artifacts of visualization program. At the beginning
distance for isopeptide bond is 1.38 Angs (and it's defined at the
specbond.dat);
LYS NZ 1 GLY C 1 0.13LYQ GLQ
together with energy minimization this distance increases to around 3.0
Angs
Hey Ahmet,
1/(N-1) sum (x-mean)(x-mean)'
is the unbiased estimator of the true (population) covariance matrix,
provided the observations are mutually independent (!)
In most cases, N is quite large, so it doesn't actually matter, and
the eigenvectors and order (not size) of the eigenvalues are i
On 2/12/13 1:12 AM, neeru sharma wrote:
Dear Gromacs Users,
I have simulated a system of protein-ion complex. As a part of the
analysis, I want to see whether there are any H-bonds or other interactions
between the active site residues and the water surrounding those residues.
I was trying to
On 2/12/13 3:30 AM, durdagis wrote:
Hello all,
I have an isopeptide bond (between Lys site chain and carboxyl terminal of
Gly) in my system and I defined this with specbond.dat and additional
residue types and I edited .rtp files using Amber ff. Although I have this
bond at the beginning (befo
On 2/12/13 6:19 AM, Abhishek Acharya wrote:
Hello Justin.
Help would really be appreciated. And yes you are correct and i
thought the same. Initially I tried using opls_345B but it didn't
work. In fact if I use opls_345B it gives me an additional error.
Anyhow here are the relevant files.
topol
Hi,
S = 1/N sum (x - ref) (x - ref)'
or
S = 1/(N-1) sum (x - ref) (x - ref)'
N: the number of frames
Which one is right?
2013/2/12 Tsjerk Wassenaar
> Hi Vivek,
>
> If you use the g_covar option -ref, you not only use the reference
> structure for fitting, you use it for calculating the devi
Hello Justin.
Help would really be appreciated. And yes you are correct and i
thought the same. Initially I tried using opls_345B but it didn't
work. In fact if I use opls_345B it gives me an additional error.
Anyhow here are the relevant files.
topology file:
# [atoms]
15 ; nr type re
Hello all,
I have an isopeptide bond (between Lys site chain and carboxyl terminal of
Gly) in my system and I defined this with specbond.dat and additional
residue types and I edited .rtp files using Amber ff. Although I have this
bond at the beginning (before pdb2gmx), it looks I need to add addi
Hi Vivek,
If you use the g_covar option -ref, you not only use the reference
structure for fitting, you use it for calculating the deviations. Your
covariance matrix is built as:
S = 1/N sum (x - ref) (x - ref)'
If you leave out the option -ref then the average structure will be
used for the cov
Last question (I hope).
How can I choose the force constant?
Indeed for the version 4.5, the force constant is defined by the
option dihre_fc in the mdp input file. After this force is multiply by
kfac contained in the dihedral_sections in the topology file
Now this option is obsolete. The f
>
>
> Message: 1
> Date: Sun, 10 Feb 2013 21:32:15 + (WET)
> From: bapti...@itqb.unl.pt
> Subject: Re: [gmx-users] Reference structure for PCA.
> To: Discussion list for GROMACS users
> Message-ID:
> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
>
Hello Antonio,
Thank you very m
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