Re: Re: Re: [gmx-users] GPU-based workstation

On Nvidia benchmarks I've found suggestions of using of the two 6 cores CPU for systems with the 2 GPU. Assuming that I'll be using two 680 GTX cards with 256 bits and 4gb ram (not a profesional nvidia cards like TESLA) what CPU's could give me the best performance- 1 i7 of 8 cores or 2 Xeons e5 w

[gmx-users] Re: QM/MM simulations

I am sending you a . topol.tpr tpr file -- View this message in context: http://gromacs.5086.x6.nabble.com/QM-MM-simulations-tp5008196p5008554.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users m

[gmx-users] Re: QM/MM simulations

I am sending you a .tpr file topol.tpr David -- View this message in context: http://gromacs.5086.x6.nabble.com/QM-MM-simulations-tp5008196p5008556.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-u

[gmx-users] FEP of ion binding protein

Dear Gmx Users, I wish to compare binding free energy obtained from US which I have sucsessfully conducted and the one obtained using FEP. Would you suggest any tutorial? Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search

[gmx-users] (no subject)

Dear all.I want to study Diffusion coefficient of carbonmonoxide in water...I get different values of force constant partial charge while searching for those constants. Can anyone help me providing the values of partial charge (of CO), force constant and lennard jones parameter used in the simul

[gmx-users] Re: FEP of ion binding protein

Hi, Steven, http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html and there is one paper"Good Practices in Free-Energy Calculations J. Phys. Chem. B, 2010, 114 (32), pp 10235–10253" Hope this data could help you! maggin -- View this message in context

[gmx-users] how to get the epsilon and sigma values of CO

Dear all.I want to study simulation of carbonmonoxide in water...I get different values of force constant partial charge while searching for those constants. Can anyone help me providing the values of partial charge (of CO), force constant and lennard jones parameter epsilon and sigma used in t

Re: [gmx-users] how to get the epsilon and sigma values of CO

if there are many values in the literature, what do you want? On Mon, May 27, 2013 at 4:29 PM, Ishwor Poudyal wrote: > Dear all.I want to study simulation of carbonmonoxide in water...I get > different values of force constant partial charge while searching for those > constants. Can anyone hel

[gmx-users] Gromacs for Non biological systems

Dear Collegues, I was pointed to Gromacs to make it work on the non biological systems. My aim is to understand the interaction of Hf precursors on Gamma Alumina surface. But, i do not know yet if gromacs can efficiently handle this. Can someone help me fiding some papers where GROMACS have been us

[gmx-users] Using many index file in one command line

Dear users, Is there command for using many different index.ndx files in one command line ? I used -n flag many times and gromacs report error. Thankful for any help! Thu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the ar

Re: [gmx-users] Re: FEP of ion binding protein

On 5/27/13 10:10 AM, maggin wrote: Hi, Steven, http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html Note that FEP (as requested in the original post) and BAR (used in the tutorial) are different methods for evaluating the free energy differences bet

Re: [gmx-users] Re: QM/MM simulations

On 5/27/13 7:17 AM, DavidPO wrote: I am sending you a .tpr file topol.tpr Thanks. I can reproduce the problem. I'll do a little digging and probably open a bug report. Compilation proceeds without any issue, though it appears to

Re: [gmx-users] Using many index file in one command line

Use make_ndx to put all your groups in one .ndx file. It's totally unnecessary to use multiple .ndx file in one command. Terry On Tue, May 28, 2013 at 10:18 AM, Kieu Thu Nguyen wrote: > Dear users, > > Is there command for using many different index.ndx files in one command > line ? I used -n

Re: [gmx-users] Using many index file in one command line

On 5/27/13 10:18 PM, Kieu Thu Nguyen wrote: Dear users, Is there command for using many different index.ndx files in one command line ? I used -n flag many times and gromacs report error. No Gromacs program accepts multiple index files simultaneously. You must specify whatever groups you

Re: [gmx-users] Using many index file in one command line

Thank Terry and Justin so much ! I got it :-) On Tue, May 28, 2013 at 9:20 AM, Justin Lemkul wrote: > > > On 5/27/13 10:18 PM, Kieu Thu Nguyen wrote: > >> Dear users, >> >> Is there command for using many different index.ndx files in one command >> line ? I used -n flag many times and gromacs r

[gmx-users] Lennard Jones parameters

Dear all I want to study the simulation of Carbonmonoxide in water. I have seen the Lennard Jones parameters, force constant and partial charges of water in the file spce.itp inherent in gromacs but couldnt get the parameters for CO .I will be pleased if anyone provide me the LJ parameters (epsilon

[gmx-users] Re: GPU-based workstation

I have nothing to contribute regarding the CPUs, but note that last week Nvidia introduced the GTX 780 GPU (a "Titan lite"), and this week it is expected to introduce the GTX 770 one (probably an "overclocked 680"). Therefore, disregarding possible price issues, it seems that the GTX 680 may not

[gmx-users] choice of forcefield

Dear all, I am a beginner to performing simulations and my system consists of protein+ cholesteryl ester +phospholipid and drug. Papers involving lipids are in general united atom, while those involving drug-protein systems are all-atom mostly. Kindly suggest me which of these, all-atom or unite

[gmx-users] ion mutation in FEP

Dear Users, I have been trying to carry out FEP calculations for a long time for mutation of Glutamine to Aspartic acid using gromacs 4.5.5. Unfortunately, some questions and problems arises during calculations. Here is the question of mine.With glutamine, the protein charge is -12. To neutralize