Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 169, Issue 67

Hi, Please don't subscribe to a digest if you actually want to discuss. Nobody will follow your replies. You already need to know what oplsaa wants for its cutoffs, so you'd best find that out from its literature before starting your work. Mark On Sat, May 19, 2018, 06:49 SHYANTANI MAITI

[gmx-users] Does a logical pressure (1 Bar) can be reached in REMD?

Dear All, I have a small system including a 4 residue peptide. I have chosen 8 temperature windows for doing REMD simulation of this system. After the temperature convergence of the 8 systems in the 1st stage of equillibration run, the obtained pressure are quite absurd, which is not change that

Re: [gmx-users] Does a logical pressure (1 Bar) can be reached in REMD?

Hi, This is normal for instantaneous measurements of pressure. See http://www.gromacs.org/Documentation/Terminology/Pressure Mark On Sat, May 19, 2018, 13:04 Soham Sarkar wrote: > Dear All, > I have a small system including a 4 residue peptide. I have chosen 8 >

Re: [gmx-users] Does a logical pressure (1 Bar) can be reached in REMD?

Thanks for reply.. but what is the actual pressure of the system? You mentioned it as the instantaneous pressure On Sat, 19 May 2018, 6:03 pm Mark Abraham, wrote: > Hi, > > This is normal for instantaneous measurements of pressure. See >

Re: [gmx-users] Does a logical pressure (1 Bar) can be reached in REMD?

On 5/19/18 8:45 AM, Soham Sarkar wrote: Thanks for reply.. but what is the actual pressure of the system? You mentioned it as the instantaneous pressure Instantaneous simply refers to the value at any given time point; these will fluctuate wildly, particularly for a tiny system like yours,

Re: [gmx-users] "energygrps" option for separating Bonded interactions

Thanks so much Justin. With regards Debdas On Fri, May 18, 2018 at 7:55 PM, Justin Lemkul wrote: > > > On 5/18/18 6:08 PM, Debdas Dhabal wrote: > >> Hi Justin, >> >> When I follow the method you suggested I am getting an error. >> (1) Using trjconv I have created a .trr file

Re: [gmx-users] Does a logical pressure (1 Bar) can be reached in REMD?

Thanks for your reply Justin... But these pressure I provided here are by doing the gmx energy -f energy.edr And then selecting the pressure from the list. It only shows these values for respective temperature windows after 1st stage of equillibration.. What should I do? How do I know what is the

Re: [gmx-users] Does a logical pressure (1 Bar) can be reached in REMD?

On 5/19/18 1:37 PM, Soham Sarkar wrote: Thanks for your reply Justin... But these pressure I provided here are by doing the gmx energy -f energy.edr And then selecting the pressure from the list. It only shows these values for respective temperature windows after 1st stage of equillibration..

[gmx-users] (no subject)

Dear all, How to modify a mdp file to generate two different tpr files, from the same initital coordinates of a Na 1.5 voltage gated channel in the membrane (it is already relaxed and in a closed state)? I need to set parameters for the system with a voltage of -80 mV and than, after 100 ns start

Re: [gmx-users] Electric field or CompEl protocol?

It's more of a philosophical question in, unfortunately. I don't use CompEl, because I believe it is conceptually clunky, but that's a matter of opinion that could turn into discussion beyond the scope of your question. I don't study biomolecules, so I can get away with applying direct fields.

[gmx-users] Electric field or CompEl protocol?

Dear all, Which protocol, Electric field section or the CompEl, I should use in the situtation: 1. I built an ion channel by homology, prepared a bilayer membrane, embeded my protein and run a simulation to relax the system (100 ns) 2. my channel was closed all the time. 3. I want to run four