I ran NPT equilibration for 1ns. Would that be ok if I rerun it for 1 or more
ns ?
Sincerely,
Shima
- Original Message -
From: Justin Lemkul
To: Discussion list for GROMACS users
Cc:
Sent: Sunday, January 6, 2013 9:15 AM
Subject: Re: [gmx-users] Fatal error: Number of atoms in Top
On 1/6/13 12:33 AM, Shima Arasteh wrote:
Do you mean that I re-run NPT step with the new index file and npt.gro (which I
got from the last NPT equilibration)? That's not clear to me yet.
That's where I'd start. You may have to run the new configuration through the
entire equilibration pro
Do you mean that I re-run NPT step with the new index file and npt.gro (which I
got from the last NPT equilibration)? That's not clear to me yet.
Thanks in advance.
Sincerely,
Shima
From: Justin Lemkul
To: Shima Arasteh ; Discussion list for GROMACS
users
@ Justin,
Thank you.
Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering
xudo...@eden.rutgers.edu
On Jan 5, 2013, at 9:15 PM, Justin Lemkul wrote:
>
>
> On 1/5/13 9:08 PM, Xu Dong Huang wrote:
>> Dear gromac users,
>>
>> If I wish to measure the distance from 1
On 1/5/13 9:08 PM, Xu Dong Huang wrote:
Dear gromac users,
If I wish to measure the distance from 1 end of my polymer to the other end,
would it be valid to use g_gyrate? Even so, does that report just the radius,
hence the function name radius of gyration?
g_polystat may be even more use
Dear gromac users,
If I wish to measure the distance from 1 end of my polymer to the other end,
would it be valid to use g_gyrate? Even so, does that report just the radius,
hence the function name radius of gyration?
Thanks,
Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of
@Justin,
Yeah I allowed the NVT to run for way too long. Therefore I get a super clumped
structure. (Where as I only wanted a slightly clumped structure). I reduced the
nsteps to about 3000 from 100 thousand to achieve my desired structure.
Thanks for the support.
Xu Dong Huang
Chemical & Bioc
@Justin,
actually. After a second thought and closer examination in VMD using RESTYPE
differentiation, maybe this is the correct output because 95% of the beads
shown are hydrophobic so they probably like to clump together after 10
time step …. I'm going to shorten my nstep in MD and see i
On 1/5/13 8:45 PM, Xu Dong Huang wrote:
for some reason my message is too long and held for approval, but anyway,
Starting Energy Minimized structure:
http://i1284.photobucket.com/albums/a571/X_huang1/ScreenShot2013-01-05at83539PM_zpsc12357ca.png
Ending NVT outcome .gro structure:
http://i1284
for some reason my message is too long and held for approval, but anyway,
Starting Energy Minimized structure:
http://i1284.photobucket.com/albums/a571/X_huang1/ScreenShot2013-01-05at83539PM_zpsc12357ca.png
Ending NVT outcome .gro structure:
http://i1284.photobucket.com/albums/a571/X_huang1/Scre
On 1/5/13 8:29 PM, Xu Dong Huang wrote:
Dear users,
I have a defined polymer .gro file and I ran energy minimization on it.
However, when I attempt to run NVT on the polymer in a vacuum (box, no
solvent), and I view the output .gro and trajectory in VMD, I see that my
polymer is no longer a
Dear users,
I have a defined polymer .gro file and I ran energy minimization on it.
However, when I attempt to run NVT on the polymer in a vacuum (box, no
solvent), and I view the output .gro and trajectory in VMD, I see that my
polymer is no longer a star, the beads are flying in every random
On 1/5/13 3:53 PM, Yutian Yang wrote:
Hi all,
I have some problems with the pressure of my system. When I try to run
equilibrium systems (NVT or NPT), I have got large pressure fluctuations (2 or
3 orders higher than average value). When I apply shear to the system, the
pressure of the sy
On 1/5/13 2:54 PM, fatemeh ramezani wrote:
HI
I'm simulating gold nanoparticle interaction with protein by oplsaa forcefield
. I added AU-AU Lennard Jones parameters to ffnonbonded.itp and also I added
what was necessary for AU atom simulation in .atp , .rtp files.
what I see After simula
On 1/5/13 3:34 PM, Parisa Rahmani wrote:
Hi gmx users,
I want to get number of helical residue as a function of time ,
but by running
g_helix -s protein.tpr -f protein_pbc.pdb -n index.ndx ,
no n-ahx.xvg output is generated.
Looking at the code, no version of Gromacs has ever produced this
> Hi all,
>
> I have some problems with the pressure of my system. When I try to run
> equilibrium systems (NVT or NPT), I have got large pressure fluctuations (2
> or 3 orders higher than average value). When I apply shear to the system, the
> pressure of the system increases with the increa
On 1/5/13 3:46 AM, Shima Arasteh wrote:
Dear all,
I have a system of POPC/Protein/water/ions to simulate. I am trying to simulate
this system by getting ideas from Justin's tutorial of kalp15-dppc.
I've passed all steps of EM, NVT, and NPT as I expected. But when I want to run
mdrun, I get s
On 1/5/13 1:45 AM, James Starlight wrote:
Justin, thanks for explanation again!
So if I understood correctly in the ffnonbonded c6 correspond to the
attraction term and c12 to the repulsion term doestn't it ? So might
Yes.
the vdw radius of the atom be increased/ deacreased via correctio
Dear all,
I have a system of POPC/Protein/water/ions to simulate. I am trying to simulate
this system by getting ideas from Justin's tutorial of kalp15-dppc.
I've passed all steps of EM, NVT, and NPT as I expected. But when I want to run
mdrun, I get some errors about waters can not be settle. S
19 matches
Mail list logo
