Hi Anirban,
Check each trajectory with gmxcheck to see whether they are okay.
Cheers,
Tsjerk
On Fri, Dec 18, 2009 at 7:32 AM, Anirban Ghosh
wrote:
> Hi ALL,
>
> I have 3 5 nano-seconds trajectory files (.trr) of a protein+lipid+water
> simulation. I am using trjcat to join them into a single .
Hi ALL,
I have 3 5 nano-seconds trajectory files (.trr) of a protein+lipid+water
simulation. I am using trjcat to join them into a single .trr file for
analysis and getting the following error:
---
ksm tprk wrote:
Hello Justin,
I looked at in my gromacs/3.3.1 and it ahs only ffgmx.n2t force field
file. because of that, I chaged to new version gromacs.
I tried to use different force filed but new version gromacs but they
didn't work.
I used gromacs/4.0.5 and I created .gro and by using
In spite of the fact that I have never used g_lie, I have used a
variety of different techniques to calculate binding free energies,
and I would be astounded if it was possible to get the precision that
you desire with only 1 ns of sampling per state. Are you sure that the
reported imprecis
On 12/17/09 9:24 PM, Marc Charendoff wrote:
Hello,
I am in the middle of using Gromacs 3.3.3 to evaulate
interaction energies between a protein and two separate ligands to
compare their binding affinities. In doing this I have run each
solvated complex through a 1 ns MD simulation and ea
ksm tprk wrote:
I changed pdb file after that I generated topology file.
It appears you are relying on grompp to figure out what parameters should be
used for these angles, and apparently, given these atom types, there are no
default values available in the force field you've chosen to use
Hello,
I am in the middle of using Gromacs 3.3.3 to evaulate interaction
energies between a protein and two separate ligands to compare their binding
affinities. In doing this I have run each solvated complex through a 1 ns MD
simulation and each solvated ligand through a 1 ns MD simulati
ksm tprk wrote:
Hello,
While I am simulating my simulations, I encountered below error.
I have pdb file which is:
HEADERPROTEIN
TITLE (5,5) Nanotube (1,1,80) replication
AUTHORTubeGen 3.3, J T Frey, University of Delaware
EXPDTATHEORETICAL MODEL
ATOM 1 C UNK 1
Hello,
While I am simulating my simulations, I encountered below error. I have pdb
file which is:
HEADERPROTEINTITLE (5,5) Nanotube (1,1,80) replicationAUTHORTubeGen
3.3, J T Frey, University of DelawareEXPDTATHEORETICAL MODELATOM 1 C
UNK 1 3.410 0.000 -98.49
Niesen, Michiel wrote:
Thank you both for the suggestions.
My system does also contain carbohydrates (sugar) and ffoplsaa.atp does
not contain the atomtypes for these molecules. Even though carbohydrate
parameters have been published for OPLS they are not present in the
ffoplsaa.atp file. I
Thank you both for the suggestions.
My system does also contain carbohydrates (sugar) and ffoplsaa.atp does not
contain the atomtypes for these molecules. Even though carbohydrate parameters
have been published for OPLS they are not present in the ffoplsaa.atp file. I
did look into the availab
Hi All:
I just wanted to add my 2 cents to the already excellent comments posted
about the conversion of different types of ion Lennard-Jones parameters,
since I get lots of emails about this very subject.
It is misleading to think of an ion parameter as a SINGLE value of sigma and
epsilon. The
Hi,
I need to know how to calculated GROMACS, the bind free energy, words,
equations used to calculated the bind free energy in the sub-program g_lie.
Thank you
Deisy Y. Rodriguez S.
Practicante de Computos Avanzados
Grupo de Investigacion en Fisicoquimica Teorica y Experimental GIFTEX
Te
On 12/17/09 5:43 PM, huikuan chao wrote:
Hi all
I am a new in using Gromacs 4
I now using g_sas to calculate the solvent accessible surface. Yet,
the outcome informs me the Vdw radius is missing for P atom in
Vdwradii.dat.
Thus I check the file and want to add the value for P. However, thou
rasoul nasiri wrote:
yes, I know there will be limitation for modeling of Folding/Unfolding
proteins with MARtini CGFF if I want to look at complete
folding/unfolding mechanism of proteins but I want to find out localized
regions of the protein (e.g. the C- or N-termini) that they have
contr
Hi all
I am a new in using Gromacs 4
I now using g_sas to calculate the solvent accessible surface. Yet, the
outcome informs me the Vdw radius is missing for P atom in Vdwradii.dat.
Thus I check the file and want to add the value for P. However, though I
read through the Manual, I can not find
yes, I know there will be limitation for modeling of Folding/Unfolding
proteins with MARtini CGFF if I want to look at complete folding/unfolding
mechanism of proteins but I want to find out localized regions of the
protein (e.g. the C- or N-termini) that they have contribution to the
denaturation
I suggest you read the original paper for Martini Protein FF. I think it is
not suitable for your purpouse.
2009/12/17 rasoul nasiri
> Hi,
>
> My purpose is finding of denaturation mechanism of proteins with MArtini
> CGFF by Gromacs.
> I mean after filling box in which there are beads of protei
Hi,
My purpose is finding of denaturation mechanism of proteins with MArtini
CGFF by Gromacs.
I mean after filling box in which there are beads of protein from water
beads with suitable van der wall distance (larger than 0.105nm), when I want
to start production phase, first switch back to the sma
rasoul nasiri wrote:
greetings GMX users,
When I use genbox command for filling solvent in CGMD simulation with
Gromacs suit, I must use a larger van der Waals distance to avoid
crashes. when I use default value (0.105nm), system will crash. Which
distance is suitable for performing CGMD simu
greetings GMX users,
When I use genbox command for filling solvent in CGMD simulation with
Gromacs suit, I must use a larger van der Waals distance to avoid crashes.
when I use default value (0.105nm), system will crash. Which distance is
suitable for performing CGMD simulation. I used 0.15 or 0.
Hi,
I am not a free private help service. Please search the GROMACS webpage
first, where your question is answered. If you have a specific problem,
please ask the mailing list.
On point, GROMACS is a simulation package, not a molecule viewer.
Mark
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