Thanks Justin for a prompt reply.
Currently I am working with 4.5.6 and CHARMM 27 as I mentioned and I was
wondering whether correct parameters can be obtained after NPT without
really upgrading the software version because some of my previous results
are obtained by working with 4.5.6 and CHARMM2
On 3/25/15 8:02 PM, Alex wrote:
I think I just googled my head off trying to find out if oplsaa supports
DNA chains, and I just can't find a definitive answer. In a 2008 post,
Justin suggested that AMBER is a better choice for DNA, but more recent
posts indicate that people casually use oplsaa
Dear users,
Rescently, I used REMD to do some simulation by Gromacs , I
konw GROMACS exchanges coordinates. So does this means every trajectory was
written at a temperture ?AND if i want to analyse the lowest temperature, can
I just analyse md0.xtc as 'trajectory no longer
I think I just googled my head off trying to find out if oplsaa supports
DNA chains, and I just can't find a definitive answer. In a 2008 post,
Justin suggested that AMBER is a better choice for DNA, but more recent
posts indicate that people casually use oplsaa with DNA (at least that's my
underst
On 3/25/15 6:52 PM, Stella Nickerson wrote:
I'm simulating a system with four different types of molecules. When I try
to look at the energies between different types of molecules, it only lists
two of the types, and lumps the other two together as "rest." As in
"BMI-rest." Why is this happenin
I'm simulating a system with four different types of molecules. When I try
to look at the energies between different types of molecules, it only lists
two of the types, and lumps the other two together as "rest." As in
"BMI-rest." Why is this happening?
Thanks,
Stella
--
Gromacs Users mailing li
On 3/25/15 3:24 PM, Priya Das wrote:
Getting high penalty ligand. str generated by Paramchem. The suggestion is
to do some validations. What steps are to be done to do these validations?
I linked the tutorial before. That is the logic of the parametrization and a
complete example. If you
On 3/25/15 2:55 PM, Rakesh Gupta wrote:
Dear gmx users
I am using berger force field for the simulation of lipid bilayers which is
combination of gromos87 and OPLS. Could any one explain how the cross non
bonded parameters (c6 and c12) were calculated in lipid.itp(
http://wcm.ucalgary.ca/tiele
On 3/25/15 2:13 PM, sridhar dwadasi wrote:
Dear Gromacs Users,
I have started to use Gromacs recently to
simulate certain properties of polymer hydrogels. I have taken Poly Vinyl
Alcohol cross linked with Glutaraldehyde as my system. In this system, I
have taken
On 3/25/15 11:17 AM, soumadwip ghosh wrote:
Dear users,
Firstly, I would like to thank Justin for helping me out
in preparing an initial system containing a single walled CNT and a ss-DNA
for MD simulations. Previously I was using position restraint as well as
freeze group f
Getting high penalty ligand. str generated by Paramchem. The suggestion is
to do some validations. What steps are to be done to do these validations?
--
*Let us all join hands to save our " Mother Earth"*
Regards,
Priya Das
Dear gmx users
I am using berger force field for the simulation of lipid bilayers which is
combination of gromos87 and OPLS. Could any one explain how the cross non
bonded parameters (c6 and c12) were calculated in lipid.itp(
http://wcm.ucalgary.ca/tieleman/downloads).
I took LP2 parameter from t
Dear Gromacs Users,
I have started to use Gromacs recently to
simulate certain properties of polymer hydrogels. I have taken Poly Vinyl
Alcohol cross linked with Glutaraldehyde as my system. In this system, I
have taken two long chains of polymers and cross linked the
Dear users,
Firstly, I would like to thank Justin for helping me out
in preparing an initial system containing a single walled CNT and a ss-DNA
for MD simulations. Previously I was using position restraint as well as
freeze group for keeping my CNT fixed during equilibration step
On 25 Mar 2015, at 11:43, rahul dhakne
mailto:rahuldhakn...@gmail.com>> wrote:
NOTE 1 [file topol.top, line 44]:
System has non-zero total charge: -163.00
Total charge should normally be an integer. See
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
for discussion on how
Dear all Gromacs user,
I minimized the energy of my DNA-protein complex with steep, l-bfgs
integrator, and then ran the mdrun with integrator = md in vacuum. Upto
energy minimization part it ran fine. When I submitted the minimized
structure for mdrun (vacuum), protein and DNA part jiggles arou
Hi Tsjerk,
First of all thanks for your quick and kind reply.
So you say that instead of using:
lipidsx[moltype] = (0, .5, 0, 0, .5, 0, 0, .5, 0,0, .5,
0,0,0, 0,0,0,0, .5, 0, 0, 0, 0, 0, 1, 1,
1, 1, 1)
lipidsy[moltype] = (0,
Hi Carlos,
Probably it's better to change the order in insane to match up with the
itp. Maybe the definition was based on a different topology than the one in
the martini_v2.0_glycolipids.itp
Alternatively, you can check up with Floris van Eerden, who used insane for
building complex glycolipid m
Dear gromacs users,
I’m planing to perform several CG simulations of different biological membranes
in the presence of an specific protein.
In order to create the membranes, i’m currently using the insane script to make
different kind of mixture (POPC alone, POPC-MGDG 5:5, POPC-SQDG 5:5, and
POP
Hi,
Perhaps "defeats the purpose" wasn't the right way to say it. But simply
> plotting the covariance matrices with arbitrary min/max is just an
> aesthetic thing, so it's not really functional. Hence why no one has coded
> that.
>
>
I disagree with that. If you have simulations of the same sy
Dear users,
I was trying to equilibrate my system containing a ssDNA,
CNT, water and some ions. I observed that it took many steps for the energy
minimization of the system and after 7/8 steps the potential finally
converged < 500 steps in a steepest descent method. Now, with that
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