[gmx-users] Optimal Hardware for Gromacs

Hi, there is a question for hardware experts. What is the optimal hardware to achieve better scalability in parallel MD simulations of 10K-100K atoms? Probably, it should be a cluster of multi-cpu, multi-core units with fast interconnection. In this case, what is the optimal=performance/price

Re: [gmx-users] Optimal Hardware for Gromacs

On 4/28/10 9:38 AM, Igor Leontyev wrote: Hi, there is a question for hardware experts. What is the optimal hardware to achieve better scalability in parallel MD simulations of 10K-100K atoms? Probably, it should be a cluster of multi-cpu, multi-core units with fast interconnection. In this

[gmx-users] simulated annealing (SA)

Hi gromacs users about SA simulation, I saw in some papers that annealing _time is very short. fpr example [The temperature was increased from 0 to 600 K over the first 4 ps, held at 600 K for 2 ps, and then slowly cooled to 0 K over 14 ps in simulation of protein-dna]. Is there limitation in

Re: [gmx-users] RDF

Hello, On 27.04.2010, at 23:31, Nilesh Dhumal wrote: Hello, I am trying to plot radial distribution function between a atom and a center of two atoms. How can I calculate the centre of two atoms and further how can I use this center to plot radial distribution funciton? you will have to

Re: [gmx-users] g_wham giving flat free energy

Michael McGovern wrote: Hi everyone. I'm having some trouble using g_wham to analyze some results. I have some simulations from gromacs 3.3 using the pull code. I'm using the latest version of g_wham to analyze the results, which the help file says is ok, using the -ip option. I've

[gmx-users] Re: how many dihedral angles should be included for the naphthalene molecule if I use oplsaa

I second Justin here, for Amber FF (which share essentially the same topology but with different parameters with OPLS/AA), the impropers dihedrals seems to be enough as for TRP. Just a side note, using ACPYPE (which uses antechamber in the core) to generate topologies for molecules like TRP, 6

[gmx-users] Freezing a portion of a protein during simulation

Hello Justin, In my topology file I am declaring: --- ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Strong position restraints on rest of B2AR #ifdef

Re: [gmx-users] Freezing a portion of a protein during simulation

Anirban Ghosh wrote: Hello Justin, In my topology file I am declaring: --- ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Strong position restraints on

Re: [gmx-users] more than one peptide in one simulation box

shahid nayeem wrote: Hi Justin Should I try to do position restraint at 500k and then full MD simulation. Always equilibrate under the conditions you wish to use prior to collecting data under those conditions. As for whether or not your force field is even valid at such high temperature

Re: [gmx-users] simulated annealing (SA)

shahab shariati wrote: Hi gromacs users about SA simulation, I saw in some papers that annealing _time is very short. fpr example [The temperature was increased from 0 to 600 K over the first 4 ps, held at 600 K for 2 ps, and then slowly cooled to 0 K over 14 ps in simulation of

[gmx-users] 1-4 interaction and Buckingham potential

Dear All, How is the 1-4 interaction treated when using Buckingham potential for vdw type of interactions in gromacs? As I understand from the manual one has to delete the [ pairs ] section in the topology file (if present) and the the scaling for 1-4 interaction will be 1.0. Did I get it

[gmx-users] implicit solvent simulation in gromacs

Hi All, I want to perform MD simulation of a protein in implicit solvent using gromacs 4.0.7. I looked into the manual but did not get any information regarding the implicit solvent. Is it avilable in gromacs? I searched in the mailing list and found someone in older mail said its not avilable.

[gmx-users] 64-bit gromacs-4.0.7 for Mac OSX

Dear all, With gromacs-4.0.5, one had the possibility to compile a 64-bit version of gromacs for Mac OS X using configure -- enable-apple-64bit. This was even suggested by configure to improve performance. With gromacs-4.0.7, the option --enable-apple-64bit of configure has disappeared and

Re: [gmx-users] 64-bit gromacs-4.0.7 for Mac OSX

J. Rui Rodrigues wrote: Dear all, With gromacs-4.0.5, one had the possibility to compile a 64-bit version of gromacs for Mac OS X using configure -- enable-apple-64bit. This was even suggested by configure to improve performance. With gromacs-4.0.7, the option --enable-apple-64bit of

Re: [gmx-users] implicit solvent simulation in gromacs

Chanchal wrote: Hi All, I want to perform MD simulation of a protein in implicit solvent using gromacs 4.0.7. I looked into the manual but did not get any information regarding the implicit solvent. Is it avilable in gromacs? I searched in the mailing list and found someone in older mail

[gmx-users] Re: g_wham giving flat free energy

Michael McGovern wrote: Hi everyone. I'm having some trouble using g_wham to analyze some results. I have some simulations from gromacs 3.3 using the pull code. I'm using the latest version of g_wham to analyze the results, which the help file says is ok, using the -ip option.

Re: [gmx-users] implicit solvent simulation in gromacs

Implicit solvent are still not available in gromacs. Using 43a1 FF is fine, except with implicit solvent! Or you should have one compatible with it! On Apr 28, 2010, at 6:27 PM, Chanchal wrote: Hi All, I want to perform MD simulation of a protein in implicit solvent using gromacs 4.0.7.

Re: [gmx-users] 64-bit gromacs-4.0.7 for Mac OSX

Hi, So, there is something going wrong here... My machine: Mac OS X 10.5.8 with 2 x 3.2 GHz Quad-Core Intel Xeon -- Compilation of gromacs against fftw3 libs installed with fink (installed in /sw/; no 64-bit libs) goes fine, but results in 32-bit binaries: tar xvzf gromacs-4.0.7.tar.gz ; cd

[gmx-users] g_wham gets stuck

Hi All, I have some problems with g_wham, and i already gone through all the postings and didn't find a hint.. basically, I'm trying to calculate PMF between two charged plates. I've performed a pulling simulation between the 2 plates according to Justin's UMBRELLA tutorial in the website (all

Re: [gmx-users] g_wham gets stuck

Amir Marcovitz wrote: Hi All, I have some problems with g_wham, and i already gone through all the postings and didn't find a hint.. For problems like these (which are hard to diagnose!), your Gromacs version, compilers used, OS, etc. would be useful. basically, I'm trying to

[gmx-users] pull distance

Dear Gromacs Users I have set my pull option as constant force and the pull geometry is distance the manual has stated that the pull_k1 unit is kJ/mol/nm . does it mean that the force applied to the protein is proportional to the distance between the 2 groups ? else what is it ? my second

[gmx-users] angle

Hello, I am doing solvation of glucose. I am trying to calculate a angle between three selected carbon atoms. If I run g_angle using angle.ndx file it consider all carbon atom. In force field C-C-C 112.5 is specified so it’s making a group of all carbon atoms. I am interested in selected carbon

Re: [gmx-users] angle

Nilesh Dhumal wrote: Hello, I am doing solvation of glucose. I am trying to calculate a angle between three selected carbon atoms. If I run g_angle using angle.ndx file it consider all carbon atom. In force field C-C-C 112.5 is specified so it’s making a group of all carbon atoms. I am

Re: [gmx-users] 64-bit gromacs-4.0.7 for Mac OSX

On 29/04/2010 5:22 AM, J. Rui Rodrigues wrote: Hi, So, there is something going wrong here... My machine: Mac OS X 10.5.8 with 2 x 3.2 GHz Quad-Core Intel Xeon -- Compilation of gromacs against fftw3 libs installed with fink (installed in /sw/; no 64-bit libs) goes fine, but results in

[gmx-users] Lincs warning

Dear gmx experts, I am having problem doing MD run for a hydrocarbon system. The system contains a stack of Hexane molecules using editconf. The distance between molecuels in the box is more than 30 A. I am wondering why I get large forces (system is blowing up) with this distance!. (LINCS

Re: [gmx-users] Lincs warning

Moeed wrote: Dear gmx experts, I am having problem doing MD run for a hydrocarbon system. The system contains a stack of Hexane molecules using editconf. The distance between molecuels in the box is more than 30 A. I am wondering why I get large forces (system is blowing up) with this

Re: [gmx-users] Freezing a portion of a protein during simulation

Hello Justin, Thanks a lot for your reply. I am using the option freezegrps in my .mdp file, given below: - ;define = -DSTRONG_POSRES define =