Good afternoon sir/ma'am,
I am using Gromacs-4.6.5 on my system (Ubuntu14.04LTS). I want to install
Gromacs-4.5.6 on the same system. I have tried to install it as tutorial
available on Gromcas site, but after sudo make install command, when I
tried to run commands:
g_rms_mod
It give error: comma
For what I know, if you open the pdb file with SPDBV il will automatically
fix the missing atoms. Then you should only take care of saving the new
structure in a new pdb and you're done!
Simone
Il 13/gen/2016 08:13, "Seera Suryanarayana" ha
scritto:
> Dear gromacs users,
>
> I have one pdb file
Dear gromacs users,
I have one pdb file which does not have one atom and I need to be fixed
that atom in the pdb to run MD simulations. Kindly suggest me to how to fix
it. Can I mutate the residue of my interest with the same residue by using
pymol or SPDBV to fix the missing atoms?
Thanks in Adv
http://vienna-ptm.univie.ac.at/
On Mon, Jan 11, 2016 at 11:11 PM, Simone Bolognini wrote:
> Thank you! Putting every hint together made the thing work perfectly! Now,
> I would be interested in performing some trial simulations in implicit
> solvent. However, GROMACS tells me that also the GBSA
Ca(2+) will block one of your binding sites, if you care.
On Tue, Jan 12, 2016 at 6:19 AM, Turgay Cakmak
wrote:
> Hi all,
>
>
> I have a quick question about neutralizing the system. I have a solvated
> system that contains a charged protein of -2q. Is there a major difference
> betwen addin
EqMD methods work poorly for highly and moderate viscous liquids.
On Tue, Jan 12, 2016 at 5:19 PM, shanmuga sundaram
wrote:
> I tried with g_energy -vis , but it calculates using einstein relation. I
> want to calculate using green kubo equation.
>
>
> regards,
>
> shanu
>
> On Tue, Jan 12,
What is the charge of your infinite periodic system if your unit cell
charge is 5e?
On Tue, Jan 12, 2016 at 11:54 AM, sun wrote:
> Hello Everyone
> I want to know how to change the non-integral charges? I am simulating a
> pentameric model of protein in water and the net charge comes out to b
On 1/12/16 3:13 PM, neda razavi wrote:
dear admins i read in kalp in dppc tutorial that we should define an strong
position restrain for protein in order to use inflateGRO. I wonder to know
whether we should use this strong position restraint for protein when using
g_membed or not?
Th
dear admins i read in kalp in dppc tutorial that we should define an strong
position restrain for protein in order to use inflateGRO. I wonder to know
whether we should use this strong position restraint for protein when using
g_membed or not?
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I tried with g_energy -vis , but it calculates using einstein relation. I
want to calculate using green kubo equation.
regards,
shanu
On Tue, Jan 12, 2016 at 12:42 AM, David van der Spoel
wrote:
> On 11/01/16 22:54, shanmuga sundaram wrote:
>
>> Hello all,
>>
>>
>> I am trying to find viscosi
On 1/12/16 9:32 AM, Hassan Aaryapour wrote:
Dear Gromacs Users,
How can I remove Zinc atoms from .xtc and .gro files after MD simulation.
Use trjconv with a suitable index group containing only the atoms you want to
keep.
-Justin
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==
Justi
Dear Gromacs Users,
How can I remove Zinc atoms from .xtc and .gro files after MD simulation.
Thanks
Hassan
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On 1/12/16 8:54 AM, sun wrote:
Hello Everyone I want to know how to change the non-integral charges? I am
simulating a pentameric model of protein in water and the net charge comes
out to be -5.0. Everything goes ok till final mdrun. As soon as its started,
it carshes. Is it dus to wring topolo
On 1/12/16 8:10 AM, ansu...@physics.iisc.ernet.in wrote:
Dear Gromacs users,
I am running an energy minimization on a protein ligand complex. The
ligand is a nucleotide and after the em the base loses its planarity. I
will be grateful if you let me know if a non-planar base is physically
possi
Hello Everyone
I want to know how to change the non-integral charges? I am simulating a
pentameric model of protein in water and the net charge comes out to be -5.0.
Everything goes ok till final mdrun. As soon as its started, it carshes. Is it
dus to wring topology as the charges are non-integr
Dear Gromacs users,
I am running an energy minimization on a protein ligand complex. The
ligand is a nucleotide and after the em the base loses its planarity. I
will be grateful if you let me know if a non-planar base is physically
possible or not. If not, what procedure i have to follow to retain
At low concentrations (just a single Ca2+) you shouldn't expect any huge
differences, though the Ca2+ may stick around the protein surface a little bit
longer than the Na+ ions which may alter how one of the charged residues is
hydrated. If the protein is of a modest size (not a small fragment),
On 1/12/16 3:19 AM, Turgay Cakmak wrote:
Hi all,
I have a quick question about neutralizing the system. I have a solvated
system that contains a charged protein of -2q. Is there a major difference
betwen adding 2 Na ions and a single Ca ion to neutralize the system
(using genion)?
For the
Hi all,
I have a quick question about neutralizing the system. I have a solvated
system that contains a charged protein of -2q. Is there a major difference
betwen adding 2 Na ions and a single Ca ion to neutralize the system
(using genion)?
Thanks in advance,
Turgay
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