Re: [gmx-users] How to add another electrostatic summation methodinGromacs

Shuangxing Dai wrote: - Original Message - From: "Mark Abraham" To: "Discussion list for GROMACS users" Sent: 27 March, 2009 5:01 PM Subject: Re: [gmx-users] How to add another electrostatic summation methodinGromacs Shuangxing Dai wrote: Yes, but I still cannot write out the pair

Re: [gmx-users] How to add another electrostatic summation methodinGromacs

- Original Message - From: "Mark Abraham" To: "Discussion list for GROMACS users" Sent: 27 March, 2009 5:01 PM Subject: Re: [gmx-users] How to add another electrostatic summation methodinGromacs Shuangxing Dai wrote: Yes, but I still cannot write out the pair interaction for each

Re: [gmx-users] How to add another electrostatic summation methodin Gromacs

Shuangxing Dai wrote: Yes, but I still cannot write out the pair interaction for each ion since there is cut off. With cut off, I need to assign a averge value of the last two constants to each ion. But I cannot get the total number of neighbours in a cut off distance in advance. So I cannot us

Re: [gmx-users] HF/6-31G** ESP derived charges to replace PRODRG assigned ones

Dear Josmar, You haven't written which force field you plan to use. For OPLS and AMBER QM-based optimisation should be fine. In Gromos, the FF was developed with the aim of reproducing experimental results and I'm not sure if you can find a better solution than examining other residues with th

Re: [gmx-users] How to add another electrostatic summation methodin Gromacs

Yes, but I still cannot write out the pair interaction for each ion since there is cut off. With cut off, I need to assign a averge value of the last two constants to each ion. But I cannot get the total number of neighbours in a cut off distance in advance. So I cannot use the user defined part

[gmx-users] HF/6-31G** ESP derived charges to replace PRODRG assigned ones

Dear users, I have been reading some posts about using externally computed charges to replace Prodrg charges at ligand topology files. Many users commented on the low trustability given to Prodrg charges (e.g http://www.mail-archive.com/gmx-users@gromacs.org/msg02360.html ; http://www.mail-arc

RE: [gmx-users] [Fwd: Problems in pulling a molecule from the membrane]

Hi, First let me say you should change to 4.0.4. I don't recall if there would be problems with your setup, but 4.0.4 has many bugfixes. I guess you problem is that you use pull_start and pull_init togther, which I guess produces double the effect you want. Please read the mdp manual. I guess y

[gmx-users] [Fwd: Problems in pulling a molecule from the membrane]

I have tested the pulling in GROMACS 4.0.2 only once and there only with 'pull_geometry = position'. But i think the problem lies in the pressure-coupling or something which is connected to it ' Step 1 Warning: pressure scaling more than 1%, mu: 1.00054 1.00054 0.83511'. Because i have not yet use

[gmx-users] localp

Hi Guys, May anyone tell me how to calculate the local pressure in a lipid bilayer using Gromacs? In this context, I knew about the existence of g_localp, but it is missed in the new versions of Gromacs. In addition, is it possible to extract the force tensor Fij for all the atom pairs of a cert

Re: [gmx-users] How to calculate PMF after AFM pulling

huifang liu wrote: Hi Justin, Thank you for your reply, but i am still a little confused. You said in principal I should be able to extract a potential of mean force from an AFM run by simply integrating the average force along the reaction coordinate and if I have the average force as a f

Re: [gmx-users] question in pulling in gromacs 4.0

anirban polley wrote: ; OPTIONS FOR WEAK COUPLING ALGORITHMS = ; Temperature coupling = Tcoupl = berendsen ; Groups to couple separately = tc-grps = DPP SOL Na PIP ; Time constant (ps) and reference temperature (K) = tau_t= 0.1 0.1

Re: [gmx-users] question in pulling in gromacs 4.0

anirban polley wrote: Hi , I want to pull a molecule from the membrane. My complete mdp file ; GENERATE VELOCITIES FOR STARTUP RUN = gen_vel = yes gen_temp = 310.0 gen_seed = 173529 Equilibrate first, then do funky things. Here, in the