Re: [gmx-users] nrexcl=3: ambiguous?

Hi, Typically 1-4 interactions are regarded as bonded interactions implementing a non-bonded functional form. So a request to exclude non-bonded interactions between atoms connected by adjacent bonds does not apply. The requirement for particular kinds of 1-4 interactions are imposed by constructi

Re: [gmx-users] Regarding No more replaceable solvent!

I have a system of 1aminoacid+511 water molecules (total is 512 molecules).and the box length is 2.52nm. So, even if i replace by 45 Na+ and 45 Cl- ions (total is 90 ions) and still i have 511-90 = 421 water molecules. and i think this is well within the solubility... How many water molecules are

Re: [gmx-users] Regarding No more replaceable solvent!

Thank you sir... Yes, I will post it in the group... Sent with Mailtrack On Mon, Feb 19, 2018 at 1

Re: [gmx-users] Regarding No more replaceable solvent!

Please be kind to respond to the list and not to my email. I believe that 3-4 water molecules get removed per ion, depending on the insertion cutoff, so with 90 x 4, you're left in a situation where there's pretty much no water left. Gromacs is actually doing you a huge favor with this error, b

Re: [gmx-users] Regarding No more replaceable solvent!

How about you actually open your 'glywi.gro' prior to adding more ions and count the number of water molecules, and then compare it with the number of ions you want to add? With concentration known and the knowledge of your box volume, this comparison shouldn't be a problem. Alex On 2/18/201

[gmx-users] Regarding No more replaceable solvent!

Hello, I added 10 Na+ and Cl- ions to the aminoacid-water system containing 512 molecules through the command gmx genion -s em.tpr -o abc.gro -p topol.top -pname NA -nname CL -np 10 -nn 10 but now, i want to increase the concentration, so i want to add 45 Na+ and Cl- ions (from calculation, the co

[gmx-users] nrexcl=3: ambiguous?

Dear Users, As mentioned in the manual, *nrexcl = 3* means "*excluding non-bonded interactions between atoms that are no further than 3 bonds away*". This means, as I understand, 1-4 interactions are also excluded. However, after simulation when "gmx energy" is used, it gives output for 1-4 inter

Re: [gmx-users] Fwd: ion channel in lipid bilayer

Hi Alex, Try either insane.py, or charmm-gui. I can't provide links, since I'm on my phone. You may need to generate the topology (itp) of the protein, which you can do with calling pdb2gmx on just the protein. You should have a topology (itp) of your favourite lipid. Peter On 18 Feb 2018 13:54

[gmx-users] Fwd: ion channel in lipid bilayer

I'm sorry for repeat, but nobody answered the question and I decided to duplicate the request. Maybe it is a problem with a form of question or its content, please, point me the mistake. Hi all! I have a question concerning immersion of the ion channel (four subunits with extracellular domains an

Re: [gmx-users] Electric Field

Hi, Suggestion, get the git version of gromacs and use git grep -i -G"electric field" src/gromacs/applied-forces Mark On Sun, Feb 18, 2018 at 7:36 PM Ali Ahmed wrote: > Dear Mark, > I could not find the electric field calculation code. In 2016 version, the > code was in mdlib/sim_util.cpp b

Re: [gmx-users] PROBLEM IN COORDINATES

Hi, The error is informative. Check the number of entries in the gro file and compare it with the [ atoms ] section in your topology, together with anything that's added under [ system ]. The total numbers need to match. Alex On 2/18/2018 11:34 AM, neelam wafa wrote: Dear gmx users, I am

Re: [gmx-users] PROBLEM IN COORDINATES

check your sol.gro if you have molecules more or less than given in your topology Best On Sun, Feb 18, 2018 at 12:34 PM, neelam wafa wrote: > Dear gmx users, > > I am doing the tutorial of protein ligand simmulation given at > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorial

Re: [gmx-users] Electric Field

Dear Mark, I could not find the electric field calculation code. In 2016 version, the code was in mdlib/sim_util.cpp but in 2018 version I could not find it. Is it elsewhere? can you tell me, please? Thanks On Fri, Jan 19, 2018 at 12:25 PM, Ali Ahmed wrote: > Dear Mark, > Thank you. this is good

[gmx-users] PROBLEM IN COORDINATES

Dear gmx users, I am doing the tutorial of protein ligand simmulation given at http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/com. when I give following command, I get an error. gmx grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr the error says the number of coordin

[gmx-users] do the results seem logical for intreaction zno nanoparticle and human serum album in gromacs?

Hi,I am studying the toxicity effect of ZnO nanoparticle (with a partial charges of +1.026 and -1.026 for Zinc and Oxygen atoms, respectively) on the Albumin structure by Gromacs. For MD simulation the nanoparticle was placed at a distance of 1nm of protein, after running pdb2gmx, the simulatio

Re: [gmx-users] Secondary structure propensity.

On 2/18/18 6:05 AM, Sundari wrote: Thank You :) I have a little doubt now. If I want total percentage of all 8 secondary structures separately i.e SS (%) than I can get this by simply averaging the propensities of ss ? No, that will give you a constant number. All residues have to be in one

Re: [gmx-users] Secondary structure propensity.

Thanks for the addition. On 16 Feb 2018 6:22 pm, "Justin Lemkul" wrote: > > > On 2/16/18 3:40 AM, Subhomoi Borkotoky wrote: > >> Hello, >> >> I believe *do_dssp* will do the trick. Generate the *.xpm* matrix file , >> it >> contains the required information. >> > > Only indirectly, but scount.xv

Re: [gmx-users] 2016H66 force field

Hi Anjana, if you use the files from 2016H66 (see my previous message) and the statement #include "ffG2016h66.itp" in your top file, no need to change anything (provided you use a correct itp file for your molecule, e.g. the CiEj on my github website). All the parameters that were changed from

Re: [gmx-users] Secondary structure propensity.

Thank You :) I have a little doubt now. If I want total percentage of all 8 secondary structures separately i.e SS (%) than I can get this by simply averaging the propensities of ss ? On Fri, Feb 16, 2018 at 6:21 PM, Justin Lemkul wrote: > > > On 2/16/18 3:40 AM, Subhomoi Borkotoky wrote: >

Re: [gmx-users] SS Content?

my problem resolved :) Thank you On Sun, Feb 18, 2018 at 4:22 PM, Sundari wrote: > Dear gromacs users, > > can any one please tell me that how we get the secondary structure > propensity or secondary structure content(%) as a function of simulation > time. > > I used "gmx do_dssp" but it gives

[gmx-users] SS Content?

Dear gromacs users, can any one please tell me that how we get the secondary structure propensity or secondary structure content(%) as a function of simulation time. I used "gmx do_dssp" but it gives me number of residues forming the secondary structure vs simulation time. is it same thing or som