Re: [gmx-users] Command not found after typing g_luck

On Aug 11, 2014 9:28 PM, Kester Wong kester2...@ibs.re.kr wrote: Dear all, I am a new GROMACS user. I have recently installed GROMACS 5.0 on Intel(R) Xeon(R) CPU X3220 with x86_64 architecture. Installation went without a problem, but I could not seem to get anything from the g_luck

[gmx-users] AVX vs AVX2

I am planning to buy an Intel Haswell-E 5820 processor which supports AVX2. I am wondering if it will have better performance than i7 4930K which supports AVX. Thank you. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List

Re: [gmx-users] Polymer not diffusing into membrane

How long is your simulation? Are you sure it is long enough to see what you want to see? On 12 Aug 2014 07:15, Alex s as1...@hotmail.com wrote: Dear Gromacs users I'm not sure if this a question suitable for this forum but I would greatly appreciate it if you can help me in anyway regarding

Re: [gmx-users] Water molecule near protein surface cannot be settled.

Actually, I managed to minimize my system. What I did was 2000 steps of minimization using l-bfgs algorithm and starting from obtain geometry it took ca. 600 steps using conjugate gradient algorithm. 2014-08-11 21:56 GMT+01:00 Mark Abraham mark.j.abra...@gmail.com: If you search, Justin has

Re: [gmx-users] Problem in Ligand-Protein complex in POPC

Thank you very much justin for your reply. But I am still facing the problem to include ligand in protein. Following step I am performing: PDB file of protein complex with ligand is taken from pdb then 1) editconf -princ -f protein.pdb -o protein_princ.pdb 2) editconf -rotate 0 0 90 -f

Re: [gmx-users] Archaeal lipid packages for Gromos 53A6

On 8/12/14, 11:08 AM, Wainwright, Josh wrote: Thanks for the prompt response Justin. We are working with protein fragments with between 1 and 3 helices. I've noticed that Anirban Ghosh made a tutorial based on yours, and he used Gromos43a1 for a GPCR (7 helices) in bacterial membranes (POPC

[gmx-users] Iron containing structure simulation crash

Hello again, I finally managed to introduce the iron into my structure and generate a topology. However, when i first run the initial energy minimization, either in vacuum or with solvent, i get the following message: It stopped because the algorithm tried to make a new step whose size was too

Re: [gmx-users] Archaeal lipid packages for Gromos 53A6

Thanks again Justin. I will try to run archaeal lipids with CHARMM36. Josh From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of gromacs.org_gmx-users-requ...@maillist.sys.kth.se

Re: [gmx-users] Iron containing structure simulation crash

On 8/12/14, 11:19 AM, Nikolaos Michelarakis wrote: Hello again, I finally managed to introduce the iron into my structure and generate a topology. However, when i first run the initial energy minimization, either in vacuum or with solvent, i get the following message: It stopped because the

Re: [gmx-users] Setting Non-bonded Scaling Constant for Amber FF

On 8/12/14, 11:57 AM, Johnny Lu wrote: Hi. I'm a first year PhD student, and wonder if we have to set the equivalent of scnb and scee (1-4 nonbond scaling facor for vdw and for electrostatic) in the gromacs mdp file when we use the Amber99SB force field in gromacs? You don't. These values

Re: [gmx-users] Iron containing structure simulation crash

An output coordinate file is always produced unless mdrun completely fails and seg faults. That doesn't mean the coordinates are sane. It's meant to help you diagnose in cases like this where you have an absurd force on some atom. What is atom 2832? What's around it? Is there anything

Re: [gmx-users] potential energy

Thanks a lot Justin. On Aug 11, 2014 10:36 PM, Meenakshi Rajput ashi.rajpu...@gmail.com wrote: thanks...can you help me out with the mdp file settings with charmm force field(proteins)? I am a new user to gromacs and stuck here. On Mon, Aug 11, 2014 at 5:07 AM, Meenakshi Rajput

Re: [gmx-users] Polymer not diffusing into membrane

I've run it for 200 ns which I think is long enough allow the polymer to diffuse. Date: Tue, 12 Aug 2014 10:41:52 +0200 From: deviceran...@gmail.com To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Polymer not diffusing into membrane How long is your simulation? Are you sure it is long

Re: [gmx-users] Setting Non-bonded Scaling Constant for Amber FF

Thanks for the answer! On Tue, Aug 12, 2014 at 12:00 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/12/14, 11:57 AM, Johnny Lu wrote: Hi. I'm a first year PhD student, and wonder if we have to set the equivalent of scnb and scee (1-4 nonbond scaling facor for vdw and for electrostatic)

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 124, Issue 58

Thank you very much for your answer! this is the link to the whole forcefield directory: https://drive.google.com/folderview?id=0Bxa-J2wEpEeqbnZDVmpmQ0JGcUEusp=sharing Since it's my first time doing something like that, i might have done something wrong in adding the iron in the forcefield.

Re: [gmx-users] Archaeal lipid packages for CHARMM36

Hello Everybody, We have now been running some tests with DPPC using the CHARMM36 forcefield like Justin suggested. We actually want to use archaeal lipids, but the lipidbook website (http://lipidbook.bioch.ox.ac.uk/package/) only seems to have archaeal parameters for Gromos53a6. Does anyone

Re: [gmx-users] Suggestions for Gromacs Perfomance

You do not show your exact hardware configuration and with different CPUs you will surely get different performance. You do not show your command line or launch configuration (#ranks, #threads, #separate PME ranks) either, but based on the -gpu_id argument you have there, I assume you are

[gmx-users] linking lipid covalently to protein...

Hello, I am trying to run a GROMACS simulation with few amino acids covalently bound to Palmitoyl-linoleylphosphatidylcholine molecules., by using GROMOS ff. I found the lipid structure and parameters on Tieleman`s website, but I don`t know how to get the parameters for covalently bound

Re: [gmx-users] treatment of electrostatics in vaccum

Hi, Cut-offs can also be more efficient, depending on the size and charge of your molecule. A periodic box that is large enough to keep periodicity artefacts negligible in vacuo may involve a huge PME grid. Kind regards, Erik On 5 Aug 2014, at 18:17, Justin Lemkul jalem...@vt.edu wrote:

Re: [gmx-users] Polymer not diffusing into membrane

On 8/12/14, 1:35 PM, Alex s wrote: I've run it for 200 ns which I think is long enough allow the polymer to diffuse. If, as you say, it never interacts or diffuses, it suggests that you're applying some sort of restraint. Without seeing .mdp files and some sort of quantitative measure

Re: [gmx-users] Polymer not diffusing into membrane

I think that may well be the case. The polymer would move freely towards and away from the bilayer in the Z direction but would never diffuse or get close enough to interact. I've just run a simulation placing the polymer in a tight space with a bilayer above and below it and theres barely any

Re: [gmx-users] potential energy

hi thanks for the charmm settings...but N atom and H atom of LYS 313 and ALA 364 are coming out of the complex. Can you tell me why is this happening? And in next positional restrained run and md simulation, charmm settings would be same or some difference should be there? On Tue, Aug 12, 2014