Re: [gmx-users] Early registration period ending for 2013 GROMACS USA Workshop and Conference

Hi Prof. Shirts, I am sure that I speak for a lot of GROMACS users when I say that I want to attend the workshop, but I cannot. I would be willing to pay the whole workshop fee (and more) if you could kindly video the whole workshop and make it available to us. Thank you. On Tue, Aug 20, 2013 at

[gmx-users] Re: GPU version of Gromacs

Dear Dwey Justin, I've not tried it yet and I've asked because in the 4.5.x GPU version of Gromacs not all features were supported. In my simulations I'm using the SD integrator and the Pull-Code. Since both are supported in the current GPU version, I will try it on a computer with a CUDA

Re: [gmx-users] Re: GPU version of Gromacs

On 8/20/13 5:52 AM, grita wrote: Dear Dwey Justin, I've not tried it yet and I've asked because in the 4.5.x GPU version of Gromacs not all features were supported. In my simulations I'm using the SD integrator and the Pull-Code. Since both are supported in the current GPU version, I will

[gmx-users] g_WHAM

Hi, I have a tpr-files.dat containing 5 tpr files as it: 4.tpr 5.tpr 6.tpr 7.tpr 8.tpr Also the pullf-files.dat is in accordance with tpr-files.dat. But when I run g_wham and visualize the histo output, I see only one curve and not 4 curves which are expected to have appropriate overlaps!

Re: [gmx-users] g_WHAM

On 8/20/13 9:59 AM, Shima Arasteh wrote: Hi, I have a tpr-files.dat containing 5 tpr files as it: 4.tpr 5.tpr 6.tpr 7.tpr 8.tpr Also the pullf-files.dat is in accordance with tpr-files.dat. But when I run g_wham and visualize the histo output, I see only one curve and not 4 curves which

Re: [gmx-users] Early registration period ending for 2013 GROMACS USA Workshop and Conference

Hi, Rajat- We are working on ways to make the workshop materials available online, either streaming or posted afterwards. The tutorials will have online components as well. We were unable to obtain travel funding for the conference this year, unfortunately! I would be willing to pay the whole

[gmx-users] Number of SOL/Water in gmx_moltype_t

Hi, I am using v-4.5.5. I have a system of DNA nucleotide *two* OH radicals solvated in water. The topology file has the following records in the end: [ molecules ] ; Compound#mols DNA_chain_X 1 SOL351 However, when I did gmxdump after running grompp, I

Re: [gmx-users] Number of SOL/Water in gmx_moltype_t

residue is a sub-field of moltype, so you are seeing that there is indeed one SOL residue per water molecule, as expected. Look elsewhere and you will see that there are 351 of those molecules recorded. The same is true of the DNA chain, but since there's only one DNA chain, the number of residues

RE: [gmx-users] Coordination number

Peak can be higher, but if it is narrower the total area can still be less. Remember it is an area under the curve. Additionally, that overall system / box density that you are using may be different too, so that will make a difference. Catch ya, Dr. Dallas Warren Drug Discovery Biology

Re: [gmx-users] Number of SOL/Water in gmx_moltype_t

What about OHN - the hydroxyl radical? I put two of them in the system to understand the issue. Under DNA_chain_X, you clearly see nr=2 for OHN. If I take one OHN out from pdb (means one DTMP, one OHN and water), I again get nr=1 for OHN. residue (2): residue[0]={name=DTMP, nr=1, ic=' '}

[gmx-users] Conversion of nm to Å

Dear Sir I have to query as to how do we convert the paramaters in nm to Å --. For example the RMSD and RMSF calculation gives result in nm. I want to convert it to Å. I request you to kindly guide me with the process Thanking You with Regards. Arunima Shilpi Ph. D Research Scholar(Cancer

RE: [gmx-users] Conversion of nm to Å

First port of call for a question like this should be a search engine http://en.wikipedia.org/wiki/Angstrom Catch ya, Dr. Dallas Warren Drug Discovery Biology Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3