Re: [gmx-users] (no subject)

I want to see the helix transition.. whether it is coming back or not in the presence of the protecting osmolyte where urea is already there in the system On Sat, 21 Jul 2018, 2:21 am Mark Abraham, wrote: > Hi, > > You haven't answered the question clearly. Do you care about observing the >

Re: [gmx-users] (no subject)

Hi, You haven't answered the question clearly. Do you care about observing the transition (whose properties will depend on how you introduce the mixing), or just the difference between before and after? Your proposed method is ill formed because you can't continue a simulation after fundamentally

Re: [gmx-users] REMD Showing Zero Exchange Probability

Hi, You can't arbitrarily choose both the temperature range and number of replicas and get non-zero exchange probability. See https://pubs.acs.org/action/showCitFormats?doi=10.1021%2Fct800016r. For a given average exchange probability, choose a range and thus the number of replicas, or the number

Re: [gmx-users] (no subject)

Dear Krieger, Frankly speaking I am planning to run a REMD for 50ns with protein urea and water in it, then after 50ns I want to add a protecting osmolyte into the system and want to continue it for another 50ns REMD so that I can have the effect of the protecting osmolyte before and after adding

Re: [gmx-users] (no subject)

Dear Mark, Sorry for late reply of your queries. Frankly speaking I am planning to run a REMD for 50ns with protein urea and water in it, then after 50ns I want to add a protecting osmolyte into the system and want to continue it for another 50ns REMD so that I can have the effect of the

Re: [gmx-users] REMD Showing Zero Exchange Probability

Hello, The REMD generator provides an estimate of the number of replicas that may be necessary (based on the system size) for performing replica exchange properly. Since you got 47 replicas, you can maybe play around with replicas more or less around that range. Maybe 16 replicas is much less for

Re: [gmx-users] REMD Showing Zero Exchange Probability

I have tried an exchange every 2 ps. That is every 1000 steps. On Fri, Jul 20, 2018 at 5:34 PM, Smith, Micholas D. wrote: > How frequently are you trying to exchange? > > === > Micholas Dean Smith, PhD. MRSC > Post-doctoral Research Associate > University of Tennessee/Oak Ridge

Re: [gmx-users] Setting correct non-bonded and pair (LJ) parameters in ffnonbonded.itp

On 7/20/18 2:42 AM, Apramita Chand wrote: Dear All, In my previous posts, I had written about errors arising upon changing the combination rule and using sigma and epsilon values. Dr Lemkul was kind enough to point out that incorrect formatting of the ffnonbonded.itp might cause errors and

Re: [gmx-users] Trouble running simulations with Nitrogen

On 7/19/18 11:54 PM, Joshua Cummings wrote: Hi Everyone, I'm currently trying to run some simulations that involve the absorption of N2 into a liquid solvent. I'm having some difficulty in generating the topology for N2. For reference, the pdb file I have for N2 is as follows: HETATM

Re: [gmx-users] REMD Showing Zero Exchange Probability

How frequently are you trying to exchange? === Micholas Dean Smith, PhD. MRSC Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics From:

[gmx-users] CNT md simulation & unusual Equilibrated structure (NVT)

Hi all, Excuse me for my questions. After energy minimization, I did NVT equilibration phase. Unfortunately, I did not find an appropriate tutorial and mdp file for CNT simulation. I used following mdp file: integrator = md nsteps = 5 dt = 0.002 energygrps = CNT LIG nstxout = 500

[gmx-users] CNT md simulation & unusual minimized structure

Dear Justin, Thanks for your answer. I rechecked box dimension (along Z) and corrected it. My problem was solved. Best, Atila -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

[gmx-users] REMD Showing Zero Exchange Probability

Dear all, I have performed REMD for a system containing Protein, Reline, Urea and Water in the temperature range 290 to 450 K consist of 16 replicas out of 47 replicas generated by REMD temperature generator. But after the MD simulation the exchange probability is zero. I have used position

Re: [gmx-users] Problems during installation

Hi Szilard, Your advice was perfect: I've installed gromacs 2018_2 on my computer and I'm currently testing some sample runs which have speeded up 20 times! However, I consistently find that mdrun only selects one GPU when two are available. Why does this happen? *nvidia-smi* Fri Jul 20

[gmx-users] Setting correct non-bonded and pair (LJ) parameters in ffnonbonded.itp

Dear All, In my previous posts, I had written about errors arising upon changing the combination rule and using sigma and epsilon values. Dr Lemkul was kind enough to point out that incorrect formatting of the ffnonbonded.itp might cause errors and that the [nonbond params] as well as [pairtypes]