Dear Justin Lemkul,
I got it. Thank you very much for your help.
Best regards,
Changwoon Jang
On Tue, Aug 30, 2016 at 8:40 PM, Chang Woon Jang
wrote:
> Dear Justin,
>
>
>Do you mean "Order of parameters"? If I would like to specify for
> table_b1.xvg, I need to set 1 after 8. If I would
Dear Justin,
Do you mean "Order of parameters"? If I would like to specify for
table_b1.xvg, I need to set 1 after 8. If I would like to specifiy for
table_b2.xvg, I need to set 2 after 8.
Am I right?
Best regards,
Changwoon Jang
On Tue, Aug 30, 2016 at 8:35 PM, Chang Woon Jang
wrote:
> D
On 8/30/16 8:35 PM, Chang Woon Jang wrote:
Dear Justin Lemkul,
I have seen the 4.2.12 and Table 5.5. However, it does not show the
specific example for several tabulated potentials in topol.top file. I
created table_b1.xvg, table_b2.xvg ... table_b5.xvg, table_a1.xvg,
table_a2.xvg ... tabl
Dear Justin Lemkul,
I have seen the 4.2.12 and Table 5.5. However, it does not show the
specific example for several tabulated potentials in topol.top file. I
created table_b1.xvg, table_b2.xvg ... table_b5.xvg, table_a1.xvg,
table_a2.xvg ... table_a6.xvg, table_d1.xvg table_d4.xvg. Those
On 8/30/16 8:11 PM, Chang Woon Jang wrote:
Dear Gromacs Users,
From the above question, I think that I need to specify the each
bonded interaction in topol.top file. Am I right?
For example,
[ bond ]
1 1 2 table_b1.xvg
2 2 3 table_b2.xvg
3 3 4 table_b3.xvg
Is this right
Dear Gromacs Users,
From the above question, I think that I need to specify the each
bonded interaction in topol.top file. Am I right?
For example,
[ bond ]
1 1 2 table_b1.xvg
2 2 3 table_b2.xvg
3 3 4 table_b3.xvg
Is this right format if I have several tabulated potential fi
Hi all
I am trying to do a Normal Mode Analysis on a protein assembly with 1.05
million atoms
without solvent or ions. I ma trying to do so using Gromacs 5.0.4 double
precision
using 1024 processor and up to 256 GB of RAM, but it always fails.
I do not get any error message from Gromacs in j
Dear Gromacs Users,
I have several bond, angle, dihedral potentials named table_b1.xvg,
table_b2.xvg, table_b3.xvg ...table_a1.xvg, table_a2.xvg ... table_d1.xvg,
table_d2.xvg, table_d3.xvg, table_d4.xvg.
In my system, there are 6 types of beads (A, B, C, D, E, F). How can I
assign each p
Hello gmx-users,
Thanks for the reply Mark.
I was going through the tutorial:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/03_workflow.html,
for setting up free energy calculations routine to apply REST2 for my
system.
I am studying folding of a small peptid
Dear Justin,
Search engine give a clue about using -nt options. However, how to
choose the proper number for -nt option from the error message?
Thank you.
Best regards,
Changwoon Jang
On Tue, Aug 30, 2016 at 12:02 PM, Justin Lemkul wrote:
>
>
> On 8/30/16 11:52 AM, Chang Woon Jang wrote:
On 8/30/16 11:52 AM, Chang Woon Jang wrote:
Dear Justin Lemkul,
Thank you for your answers. The following is the error message after I
run " gmx mdrun -s topol.tpr -c confgout.gro -o traj.trr -x traj.xtc -rdd
2.5".
Initializing Domain Decomposition on 8 ranks
Dynamic load balancing: auto
Dear Justin Lemkul,
Thank you for your answers. The following is the error message after I
run " gmx mdrun -s topol.tpr -c confgout.gro -o traj.trr -x traj.xtc -rdd
2.5".
Initializing Domain Decomposition on 8 ranks
Dynamic load balancing: auto
Will sort the charge groups at every domain (re
On 8/30/16 11:28 AM, Dan Woodall wrote:
Hello,
I'm looking to define the charges on a 10 residue polypeptide using
pdb2gmx. I want to have the N-terminus charged, and a proline at position 6
charged, but I can only find ways to assign charges to the amino acids that
typically carry charges. Is
On 8/30/16 10:41 AM, Chang Woon Jang wrote:
Dear Justin Lemkul,
Thank you for your response. Yes, I use coarse-grained system
(thermosetting polymer). I prepared the system from the equilibrated
atomistic system. The atomistic system was equilibrated using OPLS-AA force
filed under NPT and
Hello,
I'm looking to define the charges on a 10 residue polypeptide using
pdb2gmx. I want to have the N-terminus charged, and a proline at position 6
charged, but I can only find ways to assign charges to the amino acids that
typically carry charges. Is there a way I can force the program to
reco
Dear Justin Lemkul,
Thank you for your response. Yes, I use coarse-grained system
(thermosetting polymer). I prepared the system from the equilibrated
atomistic system. The atomistic system was equilibrated using OPLS-AA force
filed under NPT and NVT for almost 40 ns. The initial atomistic syst
Hi,
There is a method in gromacs to insert water molecules into a box of size
defined by you. Depending on the version of gromacs you have, it will be
something like gmx insert-molecules.
Dan
On Tuesday, August 9, 2016, Omamuyovwi Akemu
wrote:
> Dear Gromacs Users,
> I will like to do a molecu
On 8/29/16 3:10 PM, Mahboobeh Eslami wrote:
Hi all Gmx usersI want to evaluate influence of pH on the stability of
protein. can I use MD simulation for this goal? thanks
Protonate the protein and any other relevant species in different forms
characteristic of the dominant form at each g
On 8/29/16 6:02 PM, Chang Woon Jang wrote:
Dear Gromacs Users,
I have a Fatal error as follow. The error says -rdd option or -ddcheck. How
can I properly use these options? Is the following command the proper use
of these options?
gmx mdrun -s topol.tpr -c confout.gro -o traj.trr -x traj.xt
On 8/30/16 8:32 AM, Markus Kaukonen wrote:
Dear All,
I tried to get forces acting on every atom (fx, fy, fz, not the total force
on atom).
Is this somehow possible with standard gromacs 2016?
Extract them from the .trr file with gmx traj -of.
-Justin
--
=
On 8/29/16 9:20 PM, OuyangYanhua wrote:
The minimum protein-image distance is less than the value 2.0nm, such as t
around 1.6nm above. Does it mean my simulation is failed in the box size set?
Please read the first sentence of my previous reply.
-Justin
在 2016年8月29日,下午8:58,Justin Lemkul
Dear All,
I tried to get forces acting on every atom (fx, fy, fz, not the total force
on atom).
Is this somehow possible with standard gromacs 2016?
terveisin, Markus
--
--www=http://www.iki.fi/markus.kaukonen
--markus.kauko...@iki.fi
--office: www.helsinki.fi/kemia/svenskakemen/index_eng.html
--
> > Hi,
> >
> > I am trying to solvate a small DNA molecule. Since I don't want so
> >
> > simulate more waters than what is really neccessary, I decided to try the
> > dodecahdron and octahedron unit cells.
> >
> > After I added waters I went to examine the resulting structures in VMD
> >
dear all
I want to simulate a box with two walls. One of them is fixed and other is
moving with steady velocity in a certain direction. I am going to produce a
shear flow.
If I constrain wall in two directions is enough? How can I produce fixed
velocity in other direction?
Thanks,
Pari
--
Gromac
On Monday, August 29, 2016 11:40 PM, Mahboobeh Eslami
wrote:
Hi all Gmx usersI want to evaluate influence of pH on the stability of
protein. can I use MD simulation for this goal? thanks
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.or
Hi Jernej,
This is simpler in two dimensions:
Consider a hexagonal unit cell.
Draw it, together with the surrounding copies (7 hexagons total).
Now connect the central hexagon with the right horizontal neighbor, and
with the 'northeast' neighbour.
Connect these two neighbors with their other commo
Hi,
I am trying to solvate a small DNA molecule. Since I don't want so
simulate more waters than what is really neccessary, I decided to try the
dodecahdron and octahedron unit cells.
After I added waters I went to examine the resulting structures in VMD
only to find that the octahedron and do
Hi Elka,
Methyl asparagine is not known by DSSP and is not availble in Martini.
You're probably best off replacing it by asparagine:
sed '/^ATOM/s/MEN/ASN/' 1HG0.pdb > out.pdb
Cheers,
Tsjerk
On Fri, Aug 26, 2016 at 11:26 AM, Elka Firmanda wrote:
> Hi, I just got "X" amino acids on DSSP, what
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