Search found 8 matches
[phpBB Debug] PHP Warning: in file [ROOT]/vendor/twig/twig/lib/Twig/Extension/Core.php on line 1275: count(): Parameter must be an array or an object that implements Countable- Tue Aug 19, 2008 7:43 am
- Forum: Bugs
- Topic: Negative Born radii with v(z) = 2
- Replies: 3
- Views: 14069
Re: Negative Born radii with v(z) = 2
Thanks Martin, In fact I used a decreased membrane surface tension during the simulation, as well as a decreased length membrane to mimick POPC and otherwise the same values for the remaining parameters: sigma_membrane -0.03 born_mode [1=exp 2=gauss] 2 sasa_mode [0,1=v(z) 2=gauss 3=exp] 3 v(z)_mode ...
- Mon Aug 11, 2008 7:48 am
- Forum: Bugs
- Topic: Negative Born radii with v(z) = 2
- Replies: 3
- Views: 14069
Negative Born radii with v(z) = 2
During MC simulations, when using the option "v(z)_mode [1=linear 2=gauss 3=exp] 2 " I get the following message in the log.txt file: Info: negative born radius (too many terms in descreening sum - use cutoff) t = 0 rbinvf = -0.00251 (ATOM: 790 HA 90 VAL) and the calculated Born radius for atoms fro...
- Thu Aug 07, 2008 2:26 pm
- Forum: Simulation setup
- Topic: how to go from (V1,V2,V3) to U1-U6 (GROMACS type)
- Replies: 0
- Views: 23529
how to go from (V1,V2,V3) to U1-U6 (GROMACS type)
I use the following formulae to go from the V1-V3 (used in Hippo) to U1-U6 (used in GROMACS) with CA-CA-OH-HH as example: ------------------------------------------------------------ In Hippo: V1 V2 V3 For CA-CA-OH-HH : 0 1.682 0 In GROMACS U1 U2 U3 U4 U5 U6 For CA-CA-OH-HH : 7.037 0 -7.037 0 0 0 In...
- Wed Aug 06, 2008 11:16 am
- Forum: Simulation setup
- Topic: How to set up some positional constraints
- Replies: 0
- Views: 22916
How to set up some positional constraints
I am using GBIM with some explicit solvent molecules included into the active site. Is it possible to apply some positional constraints on these water molecules to prevent them to go away from the active site? I have not seen so far any way to add constraints within Hippo.
- Wed Aug 06, 2008 10:19 am
- Forum: Bugs
- Topic: TIP3P molecules included inside a cavity
- Replies: 1
- Views: 11529
TIP3P molecules included inside a cavity
I tried to include the water molecules (TIP3P) inside the active site of a target protein, but when running an MC simulation it crashed (segmentation fault). In fact all the parameters for OW-HW and HW-OW-HW were set to 0 in the file oplsaa_forcefield.dat. After correcting them I still got the same ...
- Wed Aug 06, 2008 10:11 am
- Forum: Force field parameters
- Topic: Improper Dihedrals in HIPPO
- Replies: 1
- Views: 17092
Improper Dihedrals in HIPPO
Regarding DIHEDRALS/IMPROPER DIHEDRALS. I am not sure how improper are taken into account by Hippo. Is there an easy way to go from the harmonic formulae K(theta-theta0)**2 to the V1-V3 coefficients?
- Wed Aug 06, 2008 10:08 am
- Forum: Force field parameters
- Topic: Which dihedral parameters are needed in oplsaa_forcefield
- Replies: 1
- Views: 16275
Which dihedral parameters are needed in oplsaa_forcefield
When performing some MC simulations, I added my own ligands. For one of them I had missing parameters (new atom types) and I had therefore to add them in the oplsaa_forcefield.dat file. When looking at the 'DIHEDRALTYPES:' section, it is written 'Type V1 V2 V3 V4', but in fact it seems that the para...
- Wed Aug 06, 2008 10:00 am
- Forum: Feature requests
- Topic: OpenMP numthreads option with MC simulations
- Replies: 1
- Views: 12554
OpenMP numthreads option with MC simulations
OpenMP numthreads: While performing a MC simulation I tried to change the number of threads used, but the speed was never affected [using 0,1,4 or 8]. In fact it seems that Hippo uses the maximum number of threads available on one node regardless the value of 'OpenMP numthreads'. Also, when I teste...