[gmx-users] Where can i find .itp file for aminoacid for amber03

j funct length 3 41 0.28 i think the problem is thr.itp file and its not usable for amber03 so what should i do?do you think the problem is that? i really appreciate you if you help me with regards rose Sent from my iPhone -- Gromacs Users

[gmx-users] Umbrella sampling

modify them. 2- I want that reaction coordinate across Z axes, from slab to 1.5nm far from it (and rvdw and coulomb=1.5 and rlist=1.2) but it moves from1.5nm to for example 3nm and getting closer to wall(4nm far from slab) except slab. What is my mistake?! I really need your help. Best Re

Re: [gmx-users] Distances calculation in umbrella sampling

Till nowi think the only solution is to use gmx distance for each conf.gro files.then use perl script. don't forget to delete gmx distance line from script. -Rose Sent from my iPhone > On Nov 30, 2017, at 10:28, Amir Zeb wrote: > > Hello gmx users, > > I want to ca

Re: [gmx-users] WHAM

Why you don't answer me?is there anything wrong in my question? Thank you Sent from my iPhone > On Dec 17, 2017, at 17:36, rose rahmani wrote: > > Hi, > > I try to use umbrella sampling for calculating PMF. i change distance between > protein and ZNS nanosheet. I use

Re: [gmx-users] WHAM

What you will do if you don't have a responsible professor? I tried to install GROMACS in my computer vmware>Ubuntu>... but it wasn't successful and I couldn't.Anyway, you're right I shouldn't discuss these problems here. Thanks again -Rose Sent from my iPhone &g

Re: [gmx-users] resuming run

reproduce a published finding depends on quite a > few things. > > Mark > >> On Tue, Jan 9, 2018 at 6:31 PM rose rahmani wrote: >> >> Hi; >> >> i'm doing umbrella sampling. When i compare the PMF with literature it's >> similar in TREND,

Re: [gmx-users] regarding pbc issue

You mean if -pbc could make molecule whole,everything is ok, but if not it means the molecule was broken from first, yes? Sent from my iPhone > On Jan 17, 2018, at 16:19, Justin Lemkul wrote: > > > >> On 1/17/18 5:51 AM, Vidya R wrote: >> Hi Justin, >> >> I got the same result as you said.

Re: [gmx-users] regarding pbc issue

I mean, sometimes structures may really break or collapse, in these situations trjconv won't show these broken structures whole yes? just will show them broken (as they really are) yes? Sent from my iPhone > On Jan 17, 2018, at 18:15, Justin Lemkul wrote: > > > >> O

Re: [gmx-users] regarding pbc issue

l. It happened for every AA which i pull it through sheet, so i doubt to my results. Sorry for poor english With regards Sent from my iPhone > On Jan 17, 2018, at 19:57, Justin Lemkul wrote: > > > >> On 1/17/18 11:23 AM, Rose wrote: >> I mean, sometimes structures ma

Re: [gmx-users] umbrella sampling

Sent from my iPhone > On Feb 2, 2018, at 19:01, Justin Lemkul wrote: > > > >> On 2/2/18 8:43 AM, rose rahmani wrote: >> Hi, i'm doing umbrella sampling.(pulling AA toward nanosheet).and 4nS >> simulation for each window. >> >>>

Re: [gmx-users] umbrella sampling

Thank you so much, Is it difference between using gmx tpbconv -extend 5ps OR use .gro file of last simulation as an input For new 5nS simulation?(continiuation=yes in .mdp file) Sent from my iPhone > On Feb 4, 2018, at 17:00, Justin Lemkul wrote: > > > >> On 2/2/18 10

Re: [gmx-users] umbrella sampling

at 23:30, Justin Lemkul wrote: > > > >> On 2/4/18 1:56 PM, Rose wrote: >> Thank you so much, >> Is it difference between using gmx tpbconv -extend 5ps OR use .gro file of >> last simulation as an input For new 5nS simulation?(continiuation=yes in >> .mdp

Re: [gmx-users] umbrella sampling

Sorry nothing mysterious,i'm rose(rose.rhmn93) in these all conversations, but i have some problems in my gmail which i can't open my emails every times(i don't why but it's sth related to country ip&...) because Of that i have to use my roomate account,soy aga

Re: [gmx-users] umbrella sampling

Oooh, i mean roomMate :))) Would you please answer my questions? Sent from my iPhone > On Feb 5, 2018, at 0:48, Rose wrote: > > > Sorry nothing mysterious,i'm rose(rose.rhmn93) in these all conversations, > but i have some problems in my gmail which i can't open m

[gmx-users] Umbrella sampling

Thank you so much for your detailed and useful answer,like always Honestly, this is part of my dissertation and i refer to this article mostly, which is too same.https://www.ncbi.nlm.nih.gov/pubmed/24606380 (I had to send this Message separately because Of size limitations) Sent from my iPhone

[gmx-users] Fwd: Umbrella sampling

Sent from my iPhone Begin forwarded message: > From: Rose > Date: February 5, 2018 at 1:16:29 GMT+3:30 > To: Gromacs > Subject: Umbrella sampling > > Thank you so much for your detailed and useful answer,like always > > Honestly, this is part of my dissertation and

Re: [gmx-users] Umbrella Sampling - good histogram but no result in profile

Check the size of pullf-umbrellaX files(in a directory which gmx WHAM use them). MAYBE you refer for example a wrong pullf-umbrella0 file unintentionally. It happened to me. Check the size, they should be almost close to each other. Sent from my iPhone > On Mar 14, 2018, at 18:14, Ben Tam wrot

Re: [gmx-users] Qmmm (rose rahmani)

as valid as quantum base >> calculation softwares?(sorry for being rude ;))) >> And how about this one >> >> http://cbp.cfn.kit.edu/joomla/index.php/downloads/18-gromacs-with-qm-mm-using-dftb3 >> ?is >> <http://cbp.cfn.kit.edu/joomla/index.php/down

Re: [gmx-users] is there any special tutorial for the interaction of nanosheet and amino acids?

implemented in structure.xyz file) and using smaller box with periodic boundry condition(with out using vaccum gap),are they related to each other at all?!!! Sorry for these childish questions,but I really get confused. With regards Roja > On Oct 19, 2017, at 0:08, Alex wrote: > >

Re: [gmx-users] is there any special tutorial for the interaction of nanosheet and amino acids?

When I use amber99 FF i face error which says: residue NA is not identified in force field database! -- 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 http://www.gromacs.org/Support/Mailin

[gmx-users] In the chosen force field there is no residue type for 'THR' as a standalone (starting & ending) residu

Hi GROMACS users I get the following error when i use pdb2gmx tool of GROMACS 5.4.1, with the AMBER03 ff. command: gmx pdb2gmx -f threonine.pdb -o threonine.gro -water spc error>>>In the chosen force field there is no residue type for 'THR' as a standalone (starting & ending) residue I attache

[gmx-users] In the chosen force field there is no residue type for 'THR' as a standalone (starting & ending) residue

Hi GROMACS users I get the following error when i use pdb2gmx tool of GROMACS 5.4.1, with the AMBER03 ff. command: gmx pdb2gmx -f threonine.pdb -o threonine.gro -water spc error>>>In the chosen force field there is no residue type for 'THR' as a standalone (starting & ending) residue I attache

[gmx-users] where can i find .itp file for amino acids?

j funct length 3 41 0.28 i think the problem is thr.itp file and its not usable for amber03 so what should i do?do you think the problem is that? i really appreciate you if you help me with regards rose -- Gromacs Users mailing list * Please sea

[gmx-users] itp file for aminoacids

hello how can i make an .itp file for amino acids? which amino acids is identified in AMBER forcefield? -- 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 http://www.gromacs.org/Support/Mai

Re: [gmx-users] itp file for aminoacids

gt; > <https://www.avast.com/sig-email?utm_medium=email&utm_ > > source=link&utm_campaign=sig-email&utm_content=webmail> > > Virus-free. > > www.avast.com > > <https://www.avast.com/sig-email?utm_medium=email&utm_ > > source=link&utm_campaign=s

Re: [gmx-users] itp file for aminoacids

yes of course On Mon, Oct 30, 2017 at 7:27 PM, R C Dash wrote: > can you please upload your PDB file? > > On Mon, Oct 30, 2017 at 11:41 AM, rose rahmani > wrote: > > > if it is included,so why AMBER doesnt identify amino acids like THR? > > error is such 'X'

Re: [gmx-users] itp file for aminoacids

it in that round hole. > > Mark > > On Mon, Oct 30, 2017 at 5:04 PM rose rahmani > wrote: > > > yes of course > > > > On Mon, Oct 30, 2017 at 7:27 PM, R C Dash wrote: > > > > > can you please upload your PDB file? > > > > > > On Mo

[gmx-users] Fwd: Amino acids

-- Forwarded message -- From: Rose Date: Wed, Nov 1, 2017 at 1:06 AM Subject: Amino acids To: Gromacs Hi If standalone amino acids are zwitterionic and inappropriate for AMBER and GROMACS ,what do you think about this article?! Interactions of aqueous amino acids and

[gmx-users] Amino Acids

):095101 · March 2014 DOI: 10.1063/1.4866763 · Source:PubMed <https://www.researchgate.net/publication/deref/http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpubmed%2F24606380> sorry for asking again and again With Regards Rose -- Gromacs Users mailing list * Please search the archive at http://www.groma

[gmx-users] Amino Acids

Hi If standalone amino acids are zwitterionic and inappropriate for AMBER and GROMACS ,what do you think about this article?! Interactions of aqueous amino acids and proteins with the (110) surface of ZnS in molecular dynamics simulations *Article* in The Journal of Chemical Physics 140(9):09510

[gmx-users] Amino Acids

):095101 · March 2014 DOI: 10.1063/1.4866763 · Source:PubMed <https://www.researchgate.net/publication/deref/http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpubmed%2F24606380> sorry for repeating again and again With Regards Rose -- Gromacs Users mailing list * Please search the archive at http://www.groma

Re: [gmx-users] how to do neutralization?

HI, I have the same problem,i use AMBER03 force field,the structure has Zn and S atoms and amino acids with net charge less than 1, idont know what should i do,i optimized the structure in Gaussian and put H atom for make it more stable but its not included in itp file. On Thu, Nov 2, 2017 at 1:23

Re: [gmx-users] Amino Acids

Yes,sir ;) Termini?! nothing is mentioned about it! Sent from my iPhone > On Nov 1, 2017, at 11:39, Mark Abraham wrote: > > Hi, > > Please try to keep to one email per question :-) Did you read the paper to > learn what termini they used? > > Mark > >> On W

[gmx-users] .coordinate(gro) file

both of them(like protein-ligand tutorial) but when i copy structure.gro to the end of AA.gro to make>>>complex.gro, i cant check it in any viewer like VMD,it seeems that complex.gro is not correctly modified,could you please tell me what is wrong?! Thank you Rose -- Gromacs Users mai

[gmx-users] .coordinate(gro) file

Hi I have structure.gro file 32 . . . 0ZnSS29 29 0.000 0.191 2.029 0ZnSS30 30 0.000 0.574 2.029 0ZnS Zn31 31 0.000 0.000 2.164 0ZnS Zn32 32 0.000 0.383 2.164 0.0 0.0 0.0 and AA.gro PRODRG COORDS 12 1PDB O

Re: [gmx-users] .coordinate(gro) file

Hi dear yes,i did On Mon, Nov 6, 2017 at 12:07 AM, Fitsiou, Eleni wrote: > Hi, did you change the total number of atoms in your file ? > (the second line at the top of the gro file?) > > Best, Eleni > > On 5 Nov 2017, at 20:33, rose rahmani wrote: > > > > Hi >

[gmx-users] Umbrella Sampling

r of simulation box at t=0). thank you so much best regards rose -- 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 http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe re

[gmx-users] Umbrella Sampling

ion box at t=0). thank you so much best regards rose -- 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 http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests v

[gmx-users] Umbrella Sampling

save them with the CM within each of the interval of width 0.05 nm) 2. where should i implement this " 0.1 ps " >>>what is called in mdp file? 3. how should i know that width is 0.05 between different configurations? best regards ROSE -- Gromacs Users mailing list * Pleas

[gmx-users] Umbrella Sampling

save them with the CM within each of the interval of width 0.05 nm) 2. where should i implement this " 0.1 ps " >>>what is called in mdp file? 3. how should i know that width is 0.05 between different configurations? best regards Rose -- Gromacs Users mailing list * Pleas

Re: [gmx-users] Umbrella sampling

ds Sent from my iPhone > On Nov 24, 2017, at 19:34, Justin Lemkul wrote: > > > >> On 11/24/17 9:14 AM, Rose wrote: >> Hello >> >> I'm beginner in GROMACS. I'm using umbrella sampling(helping from its >> tutorial with MR Lemkul) But I don&#x

[gmx-users] umbrella sampling

o files (0-5)? i selected them just for testing my script and to tell the truth i didn't know how use gmx distance to get all 718 (configuration's) xvg files with just ONE command so i have to get .xvg files one by one.(would you please tell me?) - it's much similar to tutorial&#x

Re: [gmx-users] Umbrella sampling

On Sat, Nov 25, 2017 at 6:57 PM, Justin Lemkul wrote: > > > On 11/24/17 3:32 PM, rose rahmani wrote: > >> I attached md_pull.mdp file >> >> i put " cutoff-scheme = group" beecause of some errors (about energy >> groups) >> > > The use o

Re: [gmx-users] umbrella sampling

On Sat, Nov 25, 2017 at 7:01 PM, Justin Lemkul wrote: > > > On 11/25/17 5:05 AM, rose rahmani wrote: > >> Hi, >> >> i'm using umbrella sampling and i'm a beginner in GROMACS. >> >> as an example i got 5 dist.xvg files and then: >> &g

Re: [gmx-users] Umbrella sampling

Sat, Nov 25, 2017 at 11:26 PM, Justin Lemkul wrote: > > > On 11/25/17 11:49 AM, rose rahmani wrote: > >> On Sat, Nov 25, 2017 at 6:57 PM, Justin Lemkul wrote: >> >> >>> On 11/24/17 3:32 PM, rose rahmani wrote: >>> >>> I attached md_pull.mdp fi

Re: [gmx-users] umbrella sampling

Sat, Nov 25, 2017 at 11:31 PM, Justin Lemkul wrote: > > > On 11/25/17 12:57 PM, rose rahmani wrote: > >> On Sat, Nov 25, 2017 at 7:01 PM, Justin Lemkul wrote: >> >> >>> On 11/25/17 5:05 AM, rose rahmani wrote: >>> >>> Hi, >>

Re: [gmx-users] Umbrella sampling

On Sat, Nov 25, 2017 at 11:46 PM, Justin Lemkul wrote: > > > On 11/25/17 3:07 PM, rose rahmani wrote: > >> Oh sorry this is .mdp file: >> >> DEFINE = -DPOSRES >> > > What are you restraining? This seems counterproductive, and by def

[gmx-users] version 16 of check point file

Hello; Which version of GROMACS use version 16 of check point file? Is version 4.5.x of GROMACS use version 12 of check point file? Best Regards Rose -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting

[gmx-users] Umbrella Sampling

Hello; what re pull_ncoords , pull_coord1_type , pull_coord1_groups (in V5.1.4) called in version 4.5.4? Thank you so much Rose -- 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] umbrella sampling

the CM by the harmonic force corresponding to the spring constant of 5000. I DON'T know how should i implement deltaZ(=2)? which .mdp option refers to it?! thank you so much Best regards Rose -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_L

Re: [gmx-users] umbrella sampling

he “pull_coord1_geometry” to “= > direction-periodic“. I prefer the former though. > > Cheers, > Alex > >> I've got it. > > would you please answer to another questions too? thank you in advance > > > > > On Sun, Nov 26, 2017 at 23:10 rose r

[gmx-users] .cpt file

Hi; Why .cpt files are not as much important as other files (since grompp works without it)? -- 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 http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Umbrella sampling

Hello; I took 2000 configuration from trajconv. Amino acid is in its normal shape till almost conf1000.gro(and a little more). But in for example conf1300.gro amino acid was disintegrated. What does it mean? Would you please help me? Best regards Rose On Sun, Nov 26, 2017 at 12:39 AM, Justin

Re: [gmx-users] Umbrella sampling

Would "pull_geometry=periodic-distance" be another solution for it? On Tue, Nov 28, 2017 at 5:11 PM, Justin Lemkul wrote: > > > On 11/28/17 12:23 AM, rose rahmani wrote: > >> Hello; >> >> I took 2000 configuration from trajconv. Amino acid is in its norm

Re: [gmx-users] umbrella sampling

On Mon, Nov 27, 2017 at 2:30 AM, rose rahmani wrote: > > > On Mon, Nov 27, 2017 at 1:55 AM, Alex wrote: > >> Hi, >> >> The answer is clearly in the error, just read it please: >> 2.848793 > 0.49 * (4/2) where 4 is the box length. >> >>> But

[gmx-users] gmx distance,umbrella sampling

Hello; would you please tell me how gmx distance calculate and write COM distance from .gro and .tpr files excactly? Best regards -Rose -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post?

[gmx-users] umbrella sampling

Hello; would you please send me Mr.lemkul's article link ? i can't find them. Thank you -- 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 http://www.gromacs.org/Support/Mailing_Lists * F

Re: [gmx-users] Umbrella sampling

On Tue, Nov 28, 2017 at 5:11 PM, Justin Lemkul wrote: > > > On 11/28/17 12:23 AM, rose rahmani wrote: > >> Hello; >> >> I took 2000 configuration from trajconv. Amino acid is in its normal shape >> till almost conf1000.gro(and a little more). But in for ex

Re: [gmx-users] Umbrella sampling

shape in EVERY steps! BUT as i told you before when i run just once in 2nS (dt=0.001 nsteps=200) periodic boundary conditions make the protein look unusual in for example conf1500.gro?!!! What happened? I've got really confused? Thank ou for your attentions -Rose On Sun, Dec 3, 2017 at 4:

[gmx-users] umbrella sampling

MX pull_group1 = Protein pull_geometry = direction pull_vec1 = 0 0 1 pull_dim= N N Y pull_rate1 = 0.0 pull_k1 = 5000 pull_start = yes pull_nstxout= 50 Best regards Rose -- Gromacs Users mailing list * Pl

Re: [gmx-users] Umbrella sampling

38e+00 -nan . . . . Would you please help me? i have not encounter this problem before Thank you so much Best regards Rose On Mon, Dec 4, 2017 at 1:55 AM, Justin Lemkul wrote: > > > On 12/3/17 8:42 AM, rose rahmani wrote: > >> I need to share you sth which just happene

Re: [gmx-users] Umbrella sampling

AM, rose rahmani wrote: > Hi, > > I try to use umbrella sampling for calculating PMF. i change distance > between protein and ZNS nanosheet. I use gomacsV4.5.4 > > after minimization and equilibration. i use: > > grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx

Re: [gmx-users] Umbrella sampling

On Sat, Dec 16, 2017 at 12:38 PM, rose rahmani wrote: > and also i want protein get closer to ZnS sheet during pulling in just Z >> direction and straightforward to sheet( like one straight line to sheet), >> is this suitable md_pull.mdp file for this approach? > > is it pos

[gmx-users] WHAM

about time?is 4nS suitable for each window?is it possible at all? Would you please help me? Best regards Rose -- 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 http://www.grom

Re: [gmx-users] WHAM

u solve it in your system, yes maybe it couldn't be the right answer for another's system but maybe a clue for someone! You have helped me many times and i really appreciate you for your attentions and kindness Thank you again dear Justin and Alex Best regards -Rose On Mon, Dec 18

[gmx-users] Density profile of water

Hello, How can i calculate density profile of water on the solid surface? I'm not sure its gmx density? or RDF? i want to calculate it on Lx *Ly Lz=0 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can'

Re: [gmx-users] Density profile of water

ns: > > http://manual.gromacs.org/programs/gmx-density.html > > Regards, > Srinivasa > > On 02/01/2018 10:20, rose rahmani wrote: > >> Hello, >> >> How can i calculate density profile of water on the solid surface? >> I'm not sure its gmx density? or R

[gmx-users] umbrella sampling, LINCS WARNING

Hello; I'm doing umbrella sampling, protein is getting closer to ZnS, but i get some step files and run crashed just 107sec to end. Would it be because of protein got very close to ZnS? Would you please help me? With regards - this is pullf.xvg 0. -0.000579208 0.0020

[gmx-users] energy minimization

Hi, I want to calculate the number of density profile of water.the initial .gro file which i have,has amino acid in itself, which should not be present in this analyze. So, i had to remove amino acid, and then, when i wanted to do energy minimization again, it's crushed and gave me step files. may

Re: [gmx-users] energy minimization

On Tue, Jan 9, 2018 at 4:31 PM, Justin Lemkul wrote: > > > On 1/6/18 10:10 AM, rose rahmani wrote: > >> Hi, >> >> I want to calculate the number of density profile of water.the initial >> .gro >> file which i have,has amino acid in itself, which shoul

[gmx-users] Time step in umbrella sampling

Hi; i'm doing umbrella sampling.i did pulling of AA from surface and then different conformation with trjconv and then umbrella sampling.i thought that 0.9 nm was the closest distance from surface because when i changed the pullratejust for 0.001 nm/ns the run crashed, so ithought it couldn't

[gmx-users] resuming run

Hi; i'm doing umbrella sampling. When i compare the PMF with literature it's similar in TREND, but peaks are not as sharp as literature( my system and literature are very similar ). if i increase the simulation time(for example from 4ns to 40ns), is there any possibility that i maybe see the sharp

[gmx-users] Umbrella Sampling-gmx distance

e Cyan Skyblue # @title "Distance" @xaxis label "Time (ps)" @yaxis label "Distance (nm)" @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend "|d|" @ s1 legen

Re: [gmx-users] Umbrella Sampling-gmx distance

0.0000.5410.000 0.0000.5410.0000.0000.5410.0000.0000.541 0.0000.0000.5410.0000.0000.5410.0000.000 0.5410.0000.0000.5410.0000.0000.5410.000 0.0000.5410.0000.0000.5410.0000.0

[gmx-users] Umbrella sampling-gmx distance

[ ZnS ] 123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45.. [ Protein ] 761 762 763 764 765 766 767 768

[gmx-users] gmx distance

Hi i'm doing umbella sampling. whenever i use gmx distance after pulling in V.5.1.4 , i wouldn't have proper dist.xvg file. I did what you said Mr.Justin ( as you refered me to this link http://manual.gromacs.org/documentation/2018-latest/user-guide/cmdline.html#g-dist) but still there are some pr

Re: [gmx-users] umbrella sampling Protein_ligand complex distance calculation

I had this problem but i couldn't solve it. But i can tell you just a temporary solution; Don't use -sep with trjconv,then use the output conf as an input for gmx distance. it probably gives you sth like this; time distances 0.0001.75372870.02386010.0428935

Re: [gmx-users] Umbrella sampling-gmx distance

rote: > > > On 1/11/18 11:38 AM, rose rahmani wrote: > >> [ ZnS ] >> 123456789 10 11 12 13 14 >> 15 >>16 17 18 19 20 21 22 23 24 25 26 27 28 29 >> 30 >>31 32 33

Re: [gmx-users] Umbrella sampling-gmx distance

27;t > provide a topology. Pass one the the -s flag. How do you want the COM to > be computed when you're not providing any masses? > > J > > On Jan 13, 2018 9:19 AM, "rose rahmani" wrote: > > > I'm relly sorry for asking you again and again but... >

[gmx-users] energy group exclusion

Hello; this is md_pull.mdp integrator = md dt = 0.002 nsteps = 100 nstxout = 5000 nstvout = 5000 nstfout = 500 nstlog = 500 nstenergy= 1000 nstxtcout

Re: [gmx-users] energy group exclusion

Yes. thank you so much On Sun, Jan 14, 2018 at 7:05 PM, Justin Lemkul wrote: > > > On 1/14/18 9:59 AM, rose rahmani wrote: > >> Hello; >> >> this is md_pull.mdp >> >> integrator = md >> dt = 0.002

[gmx-users] gmx distance

Hi, This is md_pull.mdp integrator = md dt = 0.001 nsteps = 400 nstxout = 1000 nstvout = 1000 nstfout = 500 nstlog = 500 nstenergy= 500 nstxtcout

[gmx-users] umbrella sampling

Hi, i'm doing umbrella sampling.(pulling AA toward nanosheet).and 4nS simulation for each window. >> g_energy -f umbrella0.edr -o out.xvg 1 Bond 2 Angle3 Proper-Dih. 4 Improper-Dih. 5 LJ-146 Coulomb-14 7 LJ-(SR) 8 Coulomb-(SR) 9

[gmx-users] Umbrella sampling

sheet. I did pulling and sampling manyyy times with different rates ...,still the same problem... how could it be possible?What is the problem? I really get confused. There isn't any closer distance to sample it. Would you please help me? With regards -Rose -- Gromacs Users mailing list * Ple

Re: [gmx-users] Umbrella sampling

Sorry, i can't understand, what do you mean"-zprof0" option? Could you please give me an example? On 3 Mar 2018 16:47, "Justin Lemkul" wrote: On 3/3/18 7:02 AM, rose rahmani wrote: > Hi > > I use umbrella sampling to calculate PMF, for studying the interact

[gmx-users] Separate structure from box

Hi, I want to extract a structure in a box, i mean i want to extract a sheet from the box of solution, because i dont have any separated .gro file from my sheet. How can i do that? Thank you -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] Gmx hbond

result? Is it true to compare them in this condition? With regards Rose -- 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 http://www.gromacs.org/Support/Mailing_Lists * For (un)subs

[gmx-users] Polarizability analysis

may affect all these properties? Do you have better idea? Thank you so much Rose -- 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 http://www.gromacs.org/Support/Mailing_Lists * Fo

Re: [gmx-users] force field parameters for Fe3O4?

On Fri, 13 Apr 2018, 14:35 Paul bauer, wrote: > Hello, > > I would recommend that you check relevant publications for the > simulation of magnetite if people have tried to simulate it in solvent. > I could not find anything during a short search, but maybe you'll be > more successful. :) > If the

Re: [gmx-users] force field parameters for Fe3O4?

t; interactions. > > Cheers! > > On 13/04/18 12:13, rose rahmani wrote: > > On Fri, 13 Apr 2018, 14:35 Paul bauer, wrote: > > > >> Hello, > >> > >> I would recommend that you check relevant publications for the > >> simulation of magnetit

[gmx-users] Gmx_solvate

Hi, I have input structure from my last simulation. The box is 12nm long in Z axis. There is a wall and sheet in z=3 and z=8( so z=~ 0 to 3 and z=~ 8 to 12 is empty) . I want to add solvent between z=3-8. How can i do that? The problem is that i cant adjust wall and sheet( z coordination) to star

Re: [gmx-users] Gmx_solvate

Thank you so much. You mean first use gmx solvate, then delete the Sol molecules which i dont need them? So trjorder can fix the rest, yes? On Mon, 16 Apr 2018, 16:26 Justin Lemkul, wrote: > > > On 4/16/18 5:58 AM, rose rahmani wrote: > > Hi, > > > > I have i

Re: [gmx-users] Gmx_solvate

But the box size is 4 4 12 and i should make an index for about 2000 SOL. Is there any better solution? On Mon, 16 Apr 2018, 17:34 Justin Lemkul, wrote: > > > On 4/16/18 8:51 AM, rose rahmani wrote: > > Thank you so much. > > You mean first use gmx solvate, then delete th

[gmx-users] (no subject)

Hi, I have a capped amino acid in box of water and ion(but the system is not charged) and named it initial.gro, i can see some unreal bonds when i open it with VMD(H atom has 2 bonds!). And when i open it with gaussview C and H atom where nonbobded and were single atoms around remained bonded stru

[gmx-users] Topology file for amino acid

everytime i get confused in the middle because they are little different from my need. (I ask in AMBER mailing list but there is no answer) Could you please introduce me straightforward solution or tutorial which is most simmilar to my needs? Best regards -Rose -- Gromacs Users mailing list * Please

[gmx-users] Helical structure .itp file

Hi , I want to build poly amino acids like poly threonine(ACE THR THR ... NME) BUT in its helical structure which its topology file is compatible with amber forcefield in GROMACS. Is there any way to build this structure in GROMACS? Would you please help me? Best regards -Rose -- Gromacs Users

[gmx-users] Box size

Hi, I have two nanosheet structure and they are infront of each other and about 3 nm far from each other. I have some problems in fitting the box size. I used many options triclinic, -box,... to fit the size, but it's not possible. The problem is that atoms in ZnS nanosheet are not aligned and are

Re: [gmx-users] Helical structure .itp file

Thank you somuch. I build it with anoyher software(Peptide buikder). But can i add NME and ACE terminals by GROMACS? On Mon, 7 May 2018, 19:46 Justin Lemkul, wrote: > > > On 5/7/18 11:14 AM, rose rahmani wrote: > > Hi , > > > > I want to build poly amino acids like

[gmx-users] Distribution of water polarization

Hi, How can i calculate the distribution of water polarization for example for the first two layers of water at the solid surface? How about the number of water molecules with a given polarization? I mean exactly figure2 of this article. Can gmx dipoles do it? Best regards -Rose -- Gromacs

Re: [gmx-users] Distribution of water polarization

On Fri, 11 May 2018, 19:38 Justin Lemkul, wrote: > > > On 5/11/18 11:06 AM, rose rahmani wrote: > > Hi, > > > > How can i calculate the distribution of water polarization for example > for > > the first two layers of water at the solid surface? > > &

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