Thanks a lot for your quick reply Justin. I got it.
Turgay
2012/9/7 Justin Lemkul :
>
>
> On 9/7/12 7:34 AM, Turgay Cakmak wrote:
>>
>> Hi all,
>>
>> I want to do Molecular dynamics simulation of a box of water (SPC
>> type). I get the spc216.pdb file from
Hi all,
I want to do Molecular dynamics simulation of a box of water (SPC
type). I get the spc216.pdb file from the gromacs/share/tutor.
Firstly, I did geometry optimization for nsteps= 5.
Now, can I continue with production run or do I need to do
equilibration runs to arrive correct temperatu
Hi all,
I am calculating SAS using g_sas of my system (several peptides in
water and ions, Na and Cl). I choose:
for calculation group: non-water
for output group: protein
(400 out of 750 atoms were classified as hydrophobic)
When I plot the Area vs time graphs, both the hydrop
Dear all,
Does the "number of contact calculated by g_mindist" mean that
interaction between two groups? If so, could you kindly check the
reliability of the case I have written below.
I have 10 peptides (5 of them are X-peptide and 5 of them are
Y-peptide) in a box filled with water. After MD si
starting the simulation. So in this case, is there any way to get
this interaction energy OR can I just calculate the electrostatic energy of
the whole system?
Thanks in advance,
Turgay
2012/6/8 Mark Abraham
> On 8/06/2012 11:51 PM, Turgay Cakmak wrote:
>
> Thanks Mark.
> I want
Thanks Mark.
I want to calculate Coulomb and Lennard-Jones energies using
total_dt100.edr .
But, I am not sure I can get the correct energies?
Turgay
2012/6/8 Mark Abraham
> On 8/06/2012 10:40 PM, Turgay Cakmak wrote:
>
>
> Hi all,
>
> I have encountered a problem using ene
Hi all,
I have encountered a problem using eneconv with -dt flag.
I have several energy files. Firstly, I concatenated them using the
following.
eneconv -f first.edr second.edr -settime -o total.edr
But, total.edr is so large. To reduce the size of file, I used the below
command:
e
Hi all,
I downloaded the original form of DSSP which is recently called
DSSPold. Whenever I use the following:
*do_dssp -s topol.tpr -f t raj.xtc -o ss.xpm *
It selects "Protein" by it-self without any control from me. I want to
choose from the list, for example not protein but C-alpha.
To
Hi All,
To be able to get information about the hydrophobic contacts, I prepared
index.ndx which includes 2 groups of atoms that belong to hydrophobic
residues of my system. Then, I used the command
“g_dist -f traj.xtc -s topol.tpr -n index.ndx -dist 0.4 -lt -o
lifetime.xvg” .
which gave th
Thank you for your reply. I will read the manual more carefully.
2012/6/5 Justin A. Lemkul
>
>
> On 6/5/12 4:40 AM, Turgay Cakmak wrote:
>
>>
>> Hi all,
>>
>>
>> I would like to get information about *pi-pi stacking*, *van der Waals*,
>> *el
Hi all,
I would like to get information about *pi-pi stacking*, *van der
Waals*, *electrostatic
and hydrophobic interactions* for my system (several-peptides in a box
filled with water). Can Gromacs compute these interactions?
As far as I see from mailing-list, to get information on *hydrophobi
Hi Justin,
Thank you for your quick reply. I tried to concatanete the trajectory files
4 times. Three out of four try, I got same error massage.
But it worked for the last one.. It is a weird situation.. What could cause
this?
Turgay
2012/6/1 Justin A. Lemkul
>
>
> On 6/1/12 8:02 A
Hi gromacs users,
I concatenated 7 trajectory files (each one has 10ns simulation) using
"trajcat". Then, when I used "gmxcheck", I get following error.
Reading frame 0 time0.000
# Atoms 68393
Precision 0.001 (nm)
Reading frame 13000 time 26000.000
*WARNING: Incomplete frame: nr 137
Hi Rama,
Thanks for your quick reply.
Catenate two trajectory with help of trjcat -h
to get snapshot of particular time use trjconv -dump
use appropriate pbc option
I have also used trjconv with -dump and -pbc nojump options, but still I
have same problem.
you are using -b 1 -e 1
mean
Hi Gromacs users,
I have a problem getting a snapshots using trjconv. If you could help me, I
would be very grateful. Below, I try to explain what I did and problem
happened.
Firstly, I have done 10ns long simulation (several peptides in a box). And
then, using the outputs of that simulation (conf
Hi Gromacs users,
I have a question related to the extension of the simulation.
I have done 10 ns simulation (several peptides in a box). Now, I want to
extend it 10ns more.
- As far as I see from “Justin Lemkul’s Lysozyme in water tutorial”, to
extend simulation, following should be do
Hi all,
I carried out the 120 ns simulation using Gromacs 4.5.4. Now, I want to
visualize whole trajectory (only peptides, not water molecules) at VMD.
But, I encountered the following runtime error.
Runtime error!
Program: C:\Program Files\University of Illinois\VMD\vmd.exe
abnormal program term
Hi gromacs users,
I have two different molecules, lets say A and B. I want to put 5 A
molecules and 5 B molecules in the same box.
I carried out the following steps.
1) For both A and B, I used *genbox* with *-nmol* flag separetely
and obtained the A_multiple and the B_multiple structure files
Hi all,
I am new to the Gromacs and just started to use Gromacs for MD simulations.
I am tring to extend the simulation (protein in a box) 10 ns more. For
this, I used the following command:
grompp -f md.mdp -c md_first.gro -t md_first.cpt -p topol.top -o
md_second.tpr
mdrun &
It seems to run..
I a
19 matches
Mail list logo