Re: [gmx-users] Interaction energy

On Mon, 26 Nov 2018, 21:28 Justin Lemkul > > On 11/26/18 10:51 AM, Nick Johans wrote: > > On Mon, 26 Nov 2018, 18:22 Justin Lemkul > > >> > >> On 11/22/18 11:41 AM, Nick Johans wrote: > >>> Hi > >>> > >>> I am beginner in

Re: [gmx-users] Interaction energy

On Mon, 26 Nov 2018, 18:22 Justin Lemkul > > On 11/22/18 11:41 AM, Nick Johans wrote: > > Hi > > > > I am beginner in MD. Maybe it is not a wise question but i want to > > calculate the interaction energy between protein and ligand and also PMF > in > > dif

[gmx-users] Interaction energy

Hi I am beginner in MD. Maybe it is not a wise question but i want to calculate the interaction energy between protein and ligand and also PMF in different distances. But i don't know what is the didference between PMF, i mean free energy in particular(by umbrella sampling) and the interaction ene

Re: [gmx-users] Your message to gromacs.org_gmx-users awaits moderator approval

Thank you dear justin, finally you answer me;) On Thu, 13 Sep 2018, 16:59 Justin Lemkul, wrote: > > > On 9/13/18 7:55 AM, rose rahmani wrote: > > Hi, > > > > I recieved an email from GROMACS, says the message is too big(because of > > many replies). So what should i do to continue my discussion?

Re: [gmx-users] How can i calculate the (ADF)angular distribution of the angles between water molecule water and surface?

Sorry i'm nick's friend and i couldn't access to my email so i had to send it by his account. Rose On Wed, 12 Sep 2018, 20:16 Nick Johans, wrote: > Thank you so much Joao for detailed answer. You are right, i think i > should write my own code. But since i don'

Re: [gmx-users] How can i calculate the (ADF)angular distribution of the angles between water molecule water and surface?

Thank you so much Joao for detailed answer. You are right, i think i should write my own code. But since i don't have much experience in programming, would you please introduce me some useful examples? And(see below; our former conversations) Best Rose On Wed, 12 Sep 2018, 20:04 João Henriques,

Re: [gmx-users] [BULK][EXT] Re: PDB code

rompp, my system had not integer charges, is it because of i ignore the polar groups and didn't protonate carboxyl groups? Best On Wed, 29 Aug 2018, 22:46 Justin Lemkul, wrote: > > > On 8/29/18 2:13 PM, Nick Johans wrote: > > Thank you so much Iris. > > want to sim

Re: [gmx-users] [BULK][EXT] Re: PDB code

ture_1833992660] > > Iris Nira Smith | Postdoctoral Fellow | Genomic Medicine Institute > Cleveland Clinic | 9500 Euclid Ave. / NE5-255 | Cleveland, OH 44195 | > (216) 445-7885 > > > > > From: on behalf of > Nick Johans > Reply-To: "gmx-us...@gro

Re: [gmx-users] PDB code

field parameters for protonated C-terminal carboxyl groups were used (Hong et al., 2012)." What does it mean "protonated" ? How they add H when they have used AMBER forcefield? Would you please help me? Best regards On Wed, 29 Aug 2018, 19:50 Nick Johans, wrote: > Hi, > &

[gmx-users] PDB code

Hi, I'm a beginner in GROMACS and MD. I used pdb2gmx for having topology file of PDB ID: 3e7y (lnsuline). It has 4 chains A,B,C,D after pdb2gmx. When you google it, it is mentioned that insuline has 2 chains named A,B. So why it's pdb code has 4 chains? Are they couple of each other? If yes and i

[gmx-users] restoring pullf.xvg file

Hi, I deleted the pullf.xvg file unintentionally. Is there anyway to restore and reproduce it from other outputs? Best regards -Nick -- 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 htt

Re: [gmx-users] umbrella sampling

maybe this is irrelative but i expeienced in pulling that when i decrease dt from 2fs to 1fs i could make AA much closer to Sheet (0.1 nm)in comparison with 2fs(max 0.4 nm). it's normal but these pulling runs were crushed before(when dt=2fs) so i had had to decrease nsteps or decrease pull_rate ,

Re: [gmx-users] umbrella sampling

and i have AA between sheet and wall.and it should get closer to sheet during pulling. How should i set the initial place of amino acid? it should have the minimum interaction with wall and sheet , am i right? On Fri, Feb 2, 2018 at 7:14 PM, Rose wrote: > > > Sent from my iPhone > > > On Feb 2,

Re: [gmx-users] gmx distance

Sorry, i think there is sth, maybe i've learnt wrong. let me draw it ;) | = ZnS SHEET and@=Protein conf0.gro | | |<(Z)distance=1.76--->@ t=0 | | next time if dZ=0.5 so; | | |<-(Z)distance=1.26>@ t=t1 | | next time if dZ=0.8 so; | | |<-(Z)di

[gmx-users] no residue type

Hi, i,m a beginner. i us pdb2gmx or generating topology files.this is aminoacid pdb file; ATOM 1 N HIS 1 0.102 -0.143 0.000 1.00 0.00 N ATOM 2 CA HIS 1 1.558 -0.029 0.000 1.00 0.00 C ATOM 3 C HIS 1 1.986 1.419 0.000 1.00 0.00