Hi all,
I am running a simulation of a system contains DPPC (716) and POPG (307)
lipid monolayer with CG AuNPs. In my system, I have added the counter ions
to neutralize the system and added also 0.15 M NACL (NA-136, CL-136) into
my system. After minimization, I run 6ns equilibration (Time step
First thing you should do is try it out and find out for yourself.
Far faster and far more educational for yourself.
Did you try both of those options out? What differences did you observe?
Read http://manual.gromacs.org/online/tpr.html to see why those
scripts require the tpr file. What
Dear Justin
Here is the topology file I wrote. I included all the parameters rather
than use a specific FF.
Thank you for your support
..
-
; virtual sites have zero mass
Dear all,
*1) I used following command to extend a completed simulation*
gmx convert-tpr -s md_0_1.tpr -extend 2 -o tpxout.tpr
gmx mdrun -deffnm tpxout -cpi md_0_1.cpt -v
*2) Combined the trajectories using the command*
gmx trjcat -f *.xtc -o full.xtc
*3) Now what command to use for H
Hi,
Clearly something is garbage about that last simulation, but you won't know
why until you start looking at it output. :-) Just guessing that the table
is wrong won't help you. Make a trivial system that you can use to prove
your table is right ;-)
Mark
On Mon, 17 Jul 2017 19:54 Patrick
Hello everyone,
I have created an 'alpha-helix protein embedded in a lipid bilayer’ system
using charmm-gui.
I used the mdp files provided by charmm-gui directly without changing the
number of steps or constraints for equilibration. I ran final simulation for
200 ns without any constraints
Hi all,
I am calculating the solvation energy of a LJ system, where one bead is
solvated in 1200 beads in a box. There is only LJ interaction between beads
and the interactions between beads are all the same. I calculated the free
energy with BAR method. For LJ 12-6 interaction it works well.
On 7/17/17 12:38 PM, Jivesh Madan wrote:
Hey Justin
I'm not quite well-versed with the nvt.mdp file and its components. I'm
basically trying to simulate a 3 residue ( initial- AGI, middle- AGM, final
AGF) non protein homopolymer in CHARMM36 which requires changes to be
made in the nvt.mdp
On 7/17/17 12:31 PM, Ali Ahmed wrote:
Dear Justin
I have tried same what you have said. I followed the tutorial for CO2 but
didn't work, gave an error during the energy minimization . I'm not sure
what was the wrong, I noticed the N atoms (in the box) were separated from
the virtual site after
On 7/17/17 12:17 PM, Sonia Milena Aguilera Segura wrote:
I increased the size of the simulation box to 4 nm. Indeed, the values of
pressure improved (averages around -1 bar or 1.5, 2 bar, or so). However,
the T keeps being overestimated (302 K). During NVT I got the right value,
so I
Hey Justin
I'm not quite well-versed with the nvt.mdp file and its components. I'm
basically trying to simulate a 3 residue ( initial- AGI, middle- AGM, final
AGF) non protein homopolymer in CHARMM36 which requires changes to be
made in the nvt.mdp file accordingly. I'm attaching the .pdb,
Hi all,
I am calculating the solvation energy of a LJ system, where one bead is
solvated in 1200 beads in a box. There is only LJ interaction between beads
and the interactions between beads are all the same. I calculated the free
energy with BAR method. For LJ 12-6 interaction it works well.
Dear Justin
I have tried same what you have said. I followed the tutorial for CO2 but
didn't work, gave an error during the energy minimization . I'm not sure
what was the wrong, I noticed the N atoms (in the box) were separated from
the virtual site after the error.
On Mon, Jul 17, 2017 at
1st CfP "From Virtual Reality to Immersive Analytics in Bioinformatics"
February 2018, Burlingame, California, USA
Special Session at the Stereoscopic Displays and Applications XXIX,
Burlingame, California
Special Issue of the Journal of Integrative Bioinformatics, vol 15, de
Gruyter Berlin
>>>
>>> I increased the size of the simulation box to 4 nm. Indeed, the values of
>>> pressure improved (averages around -1 bar or 1.5, 2 bar, or so). However,
>>> the T keeps being overestimated (302 K). During NVT I got the right value,
>>> so I decided to run the 200 ns NPT equilibration with
On 7/17/17 11:38 AM, Ali Ahmed wrote:
Dear Justin
Thank you very much. As I saw in some literature (as in the link below)
that N atom has a negative charge and needs a massless positive charge. I
tried with most of the FFs but could not produce nitrogen density above
critical point. I don'n
Dear Justin
Thank you very much. As I saw in some literature (as in the link below)
that N atom has a negative charge and needs a massless positive charge. I
tried with most of the FFs but could not produce nitrogen density above
critical point. I don'n know which FF is the best one and I'm new to
Hello All,
I have a question regarding the usage of gmx select.
I want to select water molecules in a particular subset in z-direction
(example z > 5 and z < 10) for each frame of my trajectory and then carry
out analysis using g_mindist on each frame of the trajectory (with
selections)
For
On 7/17/17 9:22 AM, Jivesh Madan wrote:
I was doing NVT simulations on a structure constituting of 3 monomers of
AGLC residue(glucose molecule) connected via 1-4 linkage.
Though I have modified my nvt.mdp file for CHARMM36 but still encountering
errors.
Your vdW treatment is incorrect and
On 7/16/17 9:20 PM, Ali Ahmed wrote:
Hello GROMACS users,
This is Ali, I'm new to Gromacs and doing MD simulation of nitrogen at
super critical point.The structure I use is different from regular nitrogen
(N-N). As you know N atom has a negative charge which means the nitrogen
molecule will be
On 7/15/17 5:45 AM, Chinmai P wrote:
Hi,
I have a system in which a part of my protein molecule is manually
inserted inside a liposome.
However, due to high mobility of lipids, the protein is coming out of the
liposome.
Can you please suggest ways to stabilize the system?
One way I thought
On 7/14/17 7:43 AM, farial tavakoli wrote:
Hi justin
Thank you for reply and sorry for sending in another email, because when i wanted to reply, it was rejected.Actually, since i am a new gromacs user, i used all .mdp files ( em.mdp, nvt.mdp,...) in protein-ligand complex ( lysosym 4 )
I was doing NVT simulations on a structure constituting of 3 monomers of
AGLC residue(glucose molecule) connected via 1-4 linkage.
Though I have modified my nvt.mdp file for CHARMM36 but still encountering
errors.
The following is the nvt.mdp and I am also attaching the topology file
topol.top
Hi Sudip,
I think your [mapping] section should read "gromos" instead of
"gromos54a7"; but I'm not completely sure. In addition, it could be that
your atomistic atom names need to be unique, but I'm not intimately
familiar enough with backwards to say this for sure.
Peter
On 17-07-17 13:01,
Hi Peter,
The path of my mapping file is: /home/CG2AA/Mapping/det.gromos.map
The structural sequence of my detergent is: HO-(CH2-CH2-O)8-(CH2)11-CH3
(Basically a C12EO8, i.e., polyethylene-glycol (PEG) with C12 hydrophobic
tail).
The content of det.gromos.map file is as below:
[ molecule ]
Hi Sudip,
what's the path and content of your DET mapping file?
Peter
On 17-07-17 11:41, Sudip Das wrote:
> Dear All,
>
> I forgot to mention one point in my previous mail.
>
> With the system containing only one detergent molecules gives me the
> following error, without generating any
Dear All,
I forgot to mention one point in my previous mail.
With the system containing only one detergent molecules gives me the
following error, without generating any output file.
Residues defined for transformation from martini to gromos54a7:
[]
Traceback (most recent call last):
File
Dear All,
I have carried out CGMD simulation of my system consist of a protein along
with 30 detergent molecules. I have used Martini parameters along with the
ELNEDYN model for protein.
Now I am trying to get back AA coordinates from the CG structure using
initram.sh script together with
Hi,
>I have not got any
>ramachandran plot. Kindly tell me what could be the reason.
One can point out 'n' numbers of reasons, unitill and unless the clear
information is not given.
--
Regards,
Nikhil Maroli
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