[gmx-users] epsilon_r vs. gb_epsilon_solvent

Hi, all, I have a question regarding epsilon_r value. Do I have to specify the value in .mdp file? What is the default value if I do not specify it? If I use implicit solvent, there is one parameter: gb_epsilon_solvent, which is recommended to be 80 in the manual. What is the difference between

[gmx-users] hydrogen hydrogen interaction

Hi, all, Does hydrogen hydrogen non-bond interactions be calculated in the simulation? It looks to me this kind of non-bond interaction is ignored. If not, is there a way to let it count h-h interaction? Thank you! Bo -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] Re: Re: hydrophobic and hydrophilic in implicit solvent

Hi, Thank you for your answer. May I ask where I can find the right parameter in gbsa.itp for ions? These should be very basic things in simulation, but I cannot find their parameters anywhere. How do you guys use implicit solvent if you want to have ions inside? Thank you! Bo bo.shuang wrote

[gmx-users] hydrophobic and hydrophilic in implicit solvent

Hi, all, Is that possible to define hydrophobic or hydrophilic properties in implicit solvent? Which parameter control these properties of particles? Thank you! Bo -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

Re: Re: [gmx-users] hydrophobic and hydrophilic in implicit solvent

of these particles to make them have these different properties in implicit solvent? It just an example. Hydrophobic also play important role in protein and DNA folding. That's why I want to make hydrophobic work in implicit solvent. Thank you very much for your help! Bo On 8/03/2012 2:59 AM, bo.shuang wrote

[gmx-users] Re: Re: mdrun -multi flag (Mark Abraham)

; format=flowed On 2/03/2012 10:15 AM, bo.shuang wrote: Hello, all, I am trying to do REMD simulation. So I used command: mdrun -s t2T.tpr -multi 2 -replex 1000 And gromacs gives error report: Fatal error: mdrun -multi is not supported with the thread library.Please compile GROMACS

[gmx-users] Re: Re: Re: Re: mdrun -multi flag (Mark Abraham) (Justin A. Lemkul)

Thank you for help! Is that possible to run REMD on a PC with only one processor? Bo bo.shuang wrote: Hi, Mark, Thank you for help. It works. But now I have new fatal error: Fatal error: The number of nodes (1) is not a multiple of the number of simulations (2) MPI_ABORT was invoked

[gmx-users] mdrun -multi flag

Hello, all, I am trying to do REMD simulation. So I used command: mdrun -s t2T.tpr -multi 2 -replex 1000 And gromacs gives error report: Fatal error: mdrun -multi is not supported with the thread library.Please compile GROMACS with MPI support For more information and tips for troubleshooting,

[gmx-users] change simulation temperature

Hi, all, I have a question about change the temperature in simulation. When I change the ref_t and gen_temp only, (from 300 to 400) I cannot see any difference. I am thinking if I need to change tau_t also, since diffusivity constant is also related to temperature. Am I right? Here is my mdp

[gmx-users] Re: gmx-users Digest, Vol 94, Issue 185

for GROMACS users gmx-users@gromacs.org Message-ID: 4f4d83aa.3010...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed bo.shuang wrote: Hi, all, I have a question about change the temperature in simulation. When I change the ref_t and gen_temp only, (from 300 to 400) I cannot