Hi all,
I have a very basic question regarding free energy calculations.
Free Energy change= - kTln (P/Pmin) (as also mentioned in g_sham help)
where P is the probability density
>From statistical thermodynamics we know,
entropy change = klnP
and thus enthalpy would be zero in the above case (fr
On 3/27/14, 1:59 PM, Pappu Kumar wrote:
I got two long protein complexes made out of 20 monomers of ~300 residues.
But only one complex exists biologically. I am trying to find out the
energetically favourable complex by MD simulation in gromacs 4.6.5. Initially
I took out a dimer from the comp
On 3/27/14, 7:31 PM, ookami a wrote:
I want my system to be simulated in only two dimension periodic boundary
condition. but for this one, after the pvt, everything spread in the whole
box(where z_direction is 3 times the original length of the box) and the
vacuum disappeared. so i think this s
On 3/27/14, 2:32 PM, Pappu Kumar wrote:
Thank you. Regarding g_anaeig, I basically took the eigenvectors of C-alpha
atoms of one trajectory and then projected the other trajectory on it.
Sounds reasonable.
I obtained the ATP parameters from a paper. Like all simulations, MD has some
limita
I want my system to be simulated in only two dimension periodic boundary
condition. but for this one, after the pvt, everything spread in the whole
box(where z_direction is 3 times the original length of the box) and the
vacuum disappeared. so i think this system is still simulated with xyz
dimensi
You'll have to post your image to a file sharing service, not this list.
Why do you think your result is unphysical?
Mark
On Thu, Mar 27, 2014 at 8:16 PM, ookami a wrote:
> I think I describe it wrong.
> After nvt process, my box size doesn't change but, there is no separate
> vacuum layer, a
On Mar 27, 2014 3:25 PM, "Dan Sponseller" wrote:
>
> I'm trying to prepare PEG for simulation in gromacs and running into
> considerable difficulties. My PEG chain is
>
> HOC-COC-COC..COC-COC-COH
>
> with appropriate hydrogens on the carbons. I am using the new CHARM36.ff
> Following the proce
I think I describe it wrong.
After nvt process, my box size doesn't change but, there is no separate
vacuum layer, all the molecules are spread through the whole box.
Just as the image shown. Do you know why does this happen?
Thank you very much!
On Thu, Mar 27, 2014 at 2:09 PM, ookami a wrote:
Thank you. Regarding g_anaeig, I basically took the eigenvectors of C-alpha
atoms of one trajectory and then projected the other trajectory on it.
I obtained the ATP parameters from a paper. Like all simulations, MD has some
limitations. So I don't want to highlight the things which may not be c
"failed" with the same error.
"No default Proper Dih. types"
I was trying to make an .itp file as ligand.itp and then define the
dihedral in OPLS (3) RB style. Then I kept it in the oplsaa.ff directory
and gave the path into the .top file (include). But still I'm not able to
solve this.
I'll try l
I got two long protein complexes made out of 20 monomers of ~300 residues. But
only one complex exists biologically. I am trying to find out the energetically
favourable complex by MD simulation in gromacs 4.6.5. Initially I took out a
dimer from the complexes and ran steepest descent followed b
Great, that's what I needed to know. Still, I totally agree with you. There
are certain best practices, and using a .tpr is always the best choice.
Thanks,
João
On Thu, Mar 27, 2014 at 7:02 PM, Justin Lemkul wrote:
>
>
> On 3/27/14, 1:54 PM, João Henriques wrote:
>
>> Thanks Justin. That corro
On 3/27/14, 1:54 PM, João Henriques wrote:
Thanks Justin. That corroborates my "no .tpr, no party" suspicion. However,
would it be possible to achieve a correct analysis if I were to use a whole
.gro with a properly pre-processed .xtc (-ur -pbc)? Maybe I didn't explain
myself properly, but that
Thanks Justin. That corroborates my "no .tpr, no party" suspicion. However,
would it be possible to achieve a correct analysis if I were to use a whole
.gro with a properly pre-processed .xtc (-ur -pbc)? Maybe I didn't explain
myself properly, but that's what I want to know.
/J
On Thu, Mar 27, 2
On 3/27/14, 12:16 PM, arrow50311 wrote:
Hi,
I recently got one problem with trjconv in order to keep protein whole
during post-simulation processing. The problem is my protein is a
multi-chain protein. I used dodecahedron for explicit solvent simulation.
When I use trjconv to process the data,
On 3/27/14, 1:27 PM, João Henriques wrote:
Hello everyone,
The documentation reads:
"""
All structures are fitted to the structure in the structure file. When this
is not a run input file periodicity will not be taken into account.
"""
This is rather cryptic, what does it mean in practice? N
Hello everyone,
The documentation reads:
"""
All structures are fitted to the structure in the structure file. When this
is not a run input file periodicity will not be taken into account.
"""
This is rather cryptic, what does it mean in practice? No tpr, no party?
What if I use a properly cente
Hi,
I recently got one problem with trjconv in order to keep protein whole
during post-simulation processing. The problem is my protein is a
multi-chain protein. I used dodecahedron for explicit solvent simulation.
When I use trjconv to process the data, the flag -pbc nojump -ur compact
will still
It not clear to me what compiler was used by the poster, but in my experience
nvcc works fine using gcc 4.7 (from eg macports).
Unless one runs a mac with both AVX and a CUDA capabilities, one is probably
better off with something supporting OpenMP anyway.
> CC=/opt/local/bin/gcc-mp-4.7 CXX=/opt/
I’m trying to prepare PEG for simulation in gromacs and running into
considerable difficulties. My PEG chain is
HOC-COC-COC…...COC-COC-COH
with appropriate hydrogens on the carbons. I am using the new CHARM36.ff
Following the procedure for polymers, I added a beginning, and end, and a
central cha
On 3/27/14, 9:54 AM, Dan Sponseller wrote:
I’m trying to prepare PEG for simulation in gromacs and running into
considerable difficulties. My PEG chain is
HOC-COC-COC…...COC-COC-COH
with appropriate hydrogens on the carbons. I am using the new CHARM36.ff
Following the procedure for polymers
I’m trying to prepare PEG for simulation in gromacs and running into
considerable difficulties. My PEG chain is
HOC-COC-COC…...COC-COC-COH
with appropriate hydrogens on the carbons. I am using the new CHARM36.ff
Following the procedure for polymers, I added a beginning, and end, and a
central
Or use the embarrassingly simple terminal command that a friend of mine
just recommended: sort -nk2 file
/J
On Thu, Mar 27, 2014 at 1:35 PM, João Henriques <
joao.henriques.32...@gmail.com> wrote:
> This should work in sorting a clean (no comments) xvg file by the values
> in the second col
On 3/27/14, 12:19 AM, tarak karmakar wrote:
Thanks Justin for looking at the problem.
No, the dihedral information is not written in the .top file.
I've tried to include the RB dihedral info into the 'ffbonded.itp' file but
even then it did not consider it.
Yes, the parent force field has the t
This should work in sorting a clean (no comments) xvg file by the values in
the second column. Notice this is just an example. Adapt it to your needs.
Clean comments (terminal command):
grep -v "^[#@]" dirty_rmsd.xvg > clean_rmsd.xvg
Sort stuff (script):
#!/usr/bin/env python
import numpy as np
i
On 3/27/14, 6:24 AM, Maria Astón Serrano wrote:
Dear Gromacs users
I would like to ask for your advice concerning to the input parameters for
a simulation. I am simulating a protein (1L2Y,
http://www.rcsb.org/pdb/explore/explore.do?structureId=1L2Y). I obtain the
timing results below.
R
Do you wanna sort the actual trajectory file OR just print out the sorted
frame numbers? For the latter I'd use awk, python or whatever language you
prefer to sort the rmsd.xvg file. The former would require a bit more work
around, still, it's nothing a bit of scripting can't do.
/J
On Thu, Mar
Hello!
How can I re-sort the frames of a trajectory by increasing RMSD?
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thanks for both replies ...
-DGMX_CPU_ACCELERATION=SSE2 did the trick ...
regards
michael
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Dear Gromacs users
I would like to ask for your advice concerning to the input parameters for
a simulation. I am simulating a protein (1L2Y,
http://www.rcsb.org/pdb/explore/explore.do?structureId=1L2Y). I obtain the
timing results below.
R E A L C Y C L E A N D T I M E A C C O U N T
Hello,
for the PME gromacs was giving me warnings about PME load so I putted that
values to fix warnings. I did not know this could affect accuracy.
For the .ndx file, actually I was supplying select.ndx and it can be seen
in previous mail.
I was trying to put both select.ndx and index.ndx in -n f
Your starting configuration has positions that cause aims to overlap,
causing huge LJ energies. Fix that.
Mark
On Mar 27, 2014 7:43 AM, "Lakshmi" wrote:
> Respected Sir,
>I am working with gromacs and i have got a warning as
> shown below.Can you please suggest me what to do,
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