Re: [gmx-users] Protein at given pH

Hi, Do you mean the pKa value of the side chain in solution? Or the pKa value in ethanol, DMSO, hexane? Maybe the pKa value in a membrane, or in the interior of a protein, perhaps in a hydrophobic pocket? Or the pKa with one/two/three neighbouring acidic/basic residues? If you have literature valu

Re: [gmx-users] area per lipid

I pick the snapshots every 10ns, because I don't know how much time this system needs to be simulated to reach to the proper APL. The md.mdp dile I used here is: title        = Production run for Water-POPC system ; Parameters describing the details of the NVT simulation protocol integrator  

Re: [gmx-users] constraining multiple types of bonds

Thanks Justin As you see in the .mdp file I have used SHAKE. So if I want to fix some C-C or C-O then what algorithm I have to use ? In my topology file I have specified following bonds to be constrained. The first two are covalent and the last one is M-L non-covalent bond. [ constraints ] ; ind

Re: [gmx-users] Running Gromacs in Clusters

Hi, With a fast network like Cray's you can easily get to 400-500 atoms/core core with 4.5 (that's 400+ cores for your system), perhaps even further. With 4.6 this improves quite a bit (up to 2-3x). -- Szilárd On Wed, Nov 7, 2012 at 5:19 PM, Erik Marklund wrote: > Hi, > > Sure you can go beyo

Re: [gmx-users] comparing gmx GB energy with Amber11

Hi Per I tried with single precision gmx as well. No change. Will send you input files soon. Best Sandeep On Thu, Nov 8, 2012 at 3:55 PM, Per Larsson wrote: > Hi > > Thanks for doing those test. They are all reassuring, I think. > Could you maybe send me your input-files off list and I'll tak

Re: [gmx-users] comparing gmx GB energy with Amber11

Hi Thanks for doing those test. They are all reassuring, I think. Could you maybe send me your input-files off list and I'll take a look. I suspect the issue is that different radii are being used, as Gromacs does not use the Bondi radii. Cheers /Per 8 nov 2012 kl. 16:35 skrev Sandeep Somani:

Re: [gmx-users] area per lipid

On 11/8/12 4:39 AM, Shima Arasteh wrote: Hi, I am trying to simulate POPC in water in 300 K, using charmm36 FF. In order to reach appropriate area per lipid ( 63-65 Angestroms per headgroup as mentioned in articles ), I let the system to be simulated for 40 seconds. To do so, I checked the

Re: [gmx-users] constraining multiple types of bonds

On 11/8/12 1:07 PM, tarak karmakar wrote: Dear All, In my system I need to fix three types of bonds 1) Metal-Ligand distance at a particular value given in PDB ( not covalent) These require a merged [moleculetype] and are best implemented using simple harmonic interactions (bond type 6) o

Re: [gmx-users] comparing gmx GB energy with Amber11

Hi Per Pls see inline comments: > 1. If I recall correctly, the GB-energy in gromacs is split into two > parts, GB-polarization and non-polar solvation. Can you check whether this > is the case and if the value you report is the sum of those two terms. > Yes, gromacs prints out "GB Polarization

Re: [gmx-users] GROMACS with different gcc and FFT versions but one unique *tpr file

Hi Thomas, the .tpr files you prepare should be identical if you prepare them with the same Gromacs version - regardless of the compiler. You can check that with gmxdump and a diff if you like. If you run these .tpr files using different machines or different compilers they will not be numerical

[gmx-users] GROMACS with different gcc and FFT versions but one unique *tpr file

Dear all, i have access to a cluster on which GROMACS is compiled with a different version of GCC and a different FFT libary (compared to the local machine). Will this affect simulationns if i prepare the *.tpr on the local machine and run the simulation on the cluster and the local machine? S

Re: [gmx-users] comparing gmx GB energy with Amber11

Hi A few things: 1. If I recall correctly, the GB-energy in gromacs is split into two parts, GB-polarization and non-polar solvation. Can you check whether this is the case and if the value you report is the sum of those two terms. 2. Try setting all cut-offs to 0 (infinite cutoffs). That will

Re: [gmx-users] Freeze group atoms changing position

Just as an update, I ran the simulation using position restraints with force constants set to 1 for each atom in the restrained waters, and none jumped out of the nanotube. Thanks for the help! On Thu, Nov 1, 2012 at 5:01 PM, Justin Lemkul wrote: > > > On 11/1/12 4:56 PM, Alex Marshall wrote

Re: [gmx-users] Re: Running Gromacs in Clusters

I'm gonna check all this informations, Chaban. I'm not expert in this field and I have to study much more to follow your suggestions. Soon, I return with some news. For now, thanks everyone for your suggestions. -- Marcelo Depólo Biochemistry and Molecular Biology Department University of Viçosa

Re: [gmx-users] Re:Ka/Kd

Dear All, So I went over the below Ka/Kd...Seems doesnt fit for anything, the DelG I found doesnt change for components, and just fit my data for the first 20 analysis by chance I guess, except for Ent and Enth calculations from doing PCA, which break down nicely. In case anyone reads this. I

[gmx-users] area per lipid

Hi, I am trying to simulate POPC in water in 300 K, using charmm36 FF. In order to reach appropriate area per lipid ( 63-65 Angestroms per headgroup as mentioned in articles ), I let the system to be simulated for 40 seconds. To do so, I checked the area  per lipid every 10 ns. The results of a