Dear gromacs users, I've performed umbrella sampling using 2 reaction
coordinates (of the same geometry and dimensions and which I previously
used for pulling in two phase spaces). Now I am trying to recover the PMF.
Does g_wham support this scheme? Is it correct to obtain a 1D PMF by
supplying g_w
Dear John,
Thank you very much for your advice.
Best regards,
Mijiddorj
Hi,
>
> Justin's tutorial is not a fully generalized procedure for umbrella
> sampling; it shows a workflow for one specific example which is not always
> applicable to other systems.
>
> In general, you don't have to use po
Hi,
Justin's tutorial is not a fully generalized procedure for umbrella
sampling; it shows a workflow for one specific example which is not always
applicable to other systems.
In general, you don't have to use position restraints for anything in
umbrella sampling. Justin uses them to keep the fib
Dear GMX users,
I would like to ask about position restraint during the umbrella sampling.
1. Is it need to make position restraint of lipid bilayer during the
umbrella sampling simulation?
2. The position restraint was used for the B chain of amyloid-beta peptides
in prof. Justin's tutorial. Can
On 1/15/20 6:32 AM, gmx user1 wrote:
Dear GMX users
I am doing umbrella sampling to obtain a PMF relative to the translocation
of a ligand within a membrane protein.
I want to add an harmonic potential to restrain the center of mass of the
ligand in each window ,
similarly to the protocols us
Dear GMX users
I am doing umbrella sampling to obtain a PMF relative to the translocation
of a ligand within a membrane protein.
I want to add an harmonic potential to restrain the center of mass of the
ligand in each window ,
similarly to the protocols used by Subramanian et al (
https://pubs.acs
On 11/1/19 2:09 PM, Alexander Phillips wrote:
Hello Everyone,
I am currently running a CG MARTINI simulation on a bilayer of POPC Lipid
in Water. I also have a single vitamin E in the mixture aswell (inside of
the POPC bilayer). I am trying to perform umbrella sampling by pulling the
vitamin
Hello Everyone,
I am currently running a CG MARTINI simulation on a bilayer of POPC Lipid
in Water. I also have a single vitamin E in the mixture aswell (inside of
the POPC bilayer). I am trying to perform umbrella sampling by pulling the
vitamin E and measuring it's binding energy to POPC. I am b
> Dear gromacs users,
>
> Sorry for repeating my question.
>
> I didn't receive any email so I couldn't reply and I missed
>
> them.
Hi,
Justin replied in this mail:
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2019-September/126735.html
Best,
John
>
> I am using following pull
Dear gromacs users,
Sorry for repeating my question.
I didn't receive any email so I couldn't reply and I missed
them.
I am using following pull code in md simulation
for pulling a ligand across the plasma membrane model.
Ligand passes through the membrane,but along simulation,
the size of axis
On 9/25/19 5:50 AM, Mahsa Rezaei wrote:
Dear Dr. Warren
Thanks for your response .
I made my protein-membrane system with charmm-gui.
so my force is charmm36.
I used the equilibration input files that charmm-gui provide ,
and run 400 ns simulation for equilibration of my system .
RMSD ,
Dear Dr. Warren
Unfortunately,I missed your reply!
Thanks for your response .
I made my protein-membrane system with charmm-gui.
so my force is charmm36.
I used the equilibration input files that charmm-gui provide ,
and run 400 ns simulation for equilibration of my system .
RMSD , temperatur
Dear Dr. Warren
Thanks for your response .
I made my protein-membrane system with charmm-gui.
so my force is charmm36.
I used the equilibration input files that charmm-gui provide ,
and run 400 ns simulation for equilibration of my system .
RMSD , temperature and pressure is good , so I think
Does it do that without using the pull code, i.e. just performing NPT
simulation? What is physically happening? Sounds like the bilayer is
unstable. What forcefield is this?
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash Uni
Dear gromacs users,
I am using following pull code in md simulation
for pulling a ligand across the plasma membrane model.
Ligand passes through the membrane,but along simulation,
the size of axis z increases.
My size box is 8.52807 8.52807 14.0.
And the pull distance is less than one-half
I am sorry I forgot to give the link in the last mail.
https://indianinstituteofscience-my.sharepoint.com/:f:/g/personal/pradyumn_iisc_ac_in/EkAdkzcZsepHvbE1UDJPS5UBg2mENMYsRC2S0Z2DDWS9xQ?e=3GeICo
On Fri, May 17, 2019 at 5:03 PM Pradyumn Sharma <
cherpradyumnsha...@gmail.com> wrote:
> Dear all
>
Dear all
I am trying to get a PMF for a small molecule translocation through an
asymmetric membrane. I am doing it using pull-geometry= direction to do
umbrella sampling at each window. I am getting a profile in which PMF of
molecule in the bulk water at one side of the membrane is different from
t
Dear Gromacs Users,
I would like to perform umbrella sampling on a protein using RMSD as CV.
RMSD would be measured between the simulated structure and a so called
active conformation and between an inactive conformation. To do that I am
using PLUMED. However, I am new with US simulation and I wou
On 10/22/18 1:45 PM, Dan Gil wrote:
Hello,
I am wondering if it is valid to use different force constant (k) values
between samples for umbrella sampling.
It seems that gmx_wham accepts different k values in a set, but I wanted to
make sure this is OK. Should I be wary of any artifacts with
Hello,
I am wondering if it is valid to use different force constant (k) values
between samples for umbrella sampling.
It seems that gmx_wham accepts different k values in a set, but I wanted to
make sure this is OK. Should I be wary of any artifacts with these
simulations?
Best Regards,
Dan Gi
Hi,
I did umbrella sampling for different distances of amino acid above
surface.
I found i special distance (1-1.2 nm above surface)histograms does not
overlap. I did the sampling several times even for each 0.001 nm( of the
distane between 1-1.2 nm) but the histo.xvg file didn't show ANY change
Dear All:
I am doing umbrella sampling for a dimer (Consist of two molecules
stacking together, no physical bond). I tried different force constants,
I got different PMF for each of them. Could you suggest me, How reliably
can I choose force constant. Followings are the settings:
; Pull code
p
On 7/6/18 10:42 AM, hosein geraili wrote:
Dear all,
I have a question regarding the umbrella sampling tutorial. I am using the bash script to
create the summary_distances.dat, but the problem is at first I would get the error
"Unknown command-line option -o", then I used -oh instead of -o whi
Dear all,
I have a question regarding the umbrella sampling tutorial. I am using the bash
script to create the summary_distances.dat, but the problem is at first I would
get the error "Unknown command-line option -o", then I used -oh instead of -o
which worked, but the problem is the summary_dis
On 7/4/18 6:51 AM, Chenlin Lu wrote:
Dear gromacs users,
Hello, I am doing umbrella sampling to calculate the PMF puling an Au ion out
of a protein channel. Basically, I followed the procedure given by Justin's
tutorial. The configuration generation was finished correctly and the .mdp file
Dear gromacs users,
Hello, I am doing umbrella sampling to calculate the PMF puling an Au ion out
of a protein channel. Basically, I followed the procedure given by Justin's
tutorial. The configuration generation was finished correctly and the .mdp file
summary_distance.txt are shown below:
p
Hi,
I do umbrella sampling for different distances of AA along surface and i
calculated error by bootstrapping method. Error is less than 0.5 kj.mol-1
in 0.8to1.7 nm far from surface, but in 0.6to0.8 nm error is about 2
kj.mol-1 . The minimum energy is about -5kj.mol-1 at 0.65 nm. All windows
over
Dear GROMACS users,
Currently I am experiencing a problem. At the moment I am trying to do a
umbrella sampling with water going through a porous material. I have generate
the configuration based on CV direction (1,1,1).
However when I watch the movie back for individual simulation. I see the wa
Okay. Thanks Justin!
On 27.03.2018 21:12, Justin Lemkul wrote:
On 3/27/18 4:44 AM, Hermann, Johannes wrote:
Dear All, dear Justin,
I am playing around with my umbrella sampling setup and I was looking
at your paper which you linked in your umbrella sampling tutorial
("Assessing the Stabil
On 3/27/18 4:44 AM, Hermann, Johannes wrote:
Dear All, dear Justin,
I am playing around with my umbrella sampling setup and I was looking
at your paper which you linked in your umbrella sampling tutorial
("Assessing the Stability of Alzheimer’s Amyloid Protofibrils Using
Molecular Dynamics"
Dear All, dear Justin,
I am playing around with my umbrella sampling setup and I was looking at
your paper which you linked in your umbrella sampling tutorial
("Assessing the Stability of Alzheimer’s Amyloid Protofibrils Using
Molecular Dynamics").
Up to a distance of 2nm you use a 0.1nm spaci
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
lps,
Jochen
Thank you very much,
Ben
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of Awasthi, Neha
Sent: Wednesday, March 14, 2018 15:16
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Umbrella Sampling - good histogram but no result in
pr
om: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of Awasthi, Neha
Sent: Wednesday, March 14, 2018 15:16
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Umbrella Sampling - good histogram but no result in
profile
Before labeling this as a bug and reporting on redmine, I sugges
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of Mark Abraham
Sent: Wednesday, March 14, 2018 3:51 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Umbrella Sampling - good histogram but no result in
profile
Hi,
That would generally suggest something divided by zero, or similar
Hi,
That would generally suggest something divided by zero, or similar, eg
because no data was in a histogram bin, etc.
That behavior is a bug that we could perhaps fix if you would be so kind as
to report it at https://redmine.gromacs.org.
But the core problem remains that something about how y
Dear all,
I have a rather strange problem. Currently I am trying to get a PMF of a water
molecule through a hydrophobic materials. At the end of using "gmx wham", I get
a rather good histogram and it cover the whole range of the system. However at
the making profile.xvg. I get the answer "nan"
On 3/3/18 9:27 AM, rose rahmani wrote:
Sorry, i can't understand, what do you mean"-zprof0" option? Could you
please give me an example?
Please read the gmx wham help information for a description.
-Justin
On 3 Mar 2018 16:47, "Justin Lemkul" wrote:
On 3/3/18 7:02 AM, rose rahmani wrot
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 interaction of
> different aminoacids with n
On 3/3/18 7:02 AM, rose rahmani wrote:
Hi
I use umbrella sampling to calculate PMF, for studying the interaction of
different aminoacids with nanosheet separately. But at the minimum distance
from sheet, potential is zero for all PMF diagrams. I mean there isn't any
positive potential even at
Hi
I use umbrella sampling to calculate PMF, for studying the interaction of
different aminoacids with nanosheet separately. But at the minimum distance
from sheet, potential is zero for all PMF diagrams. I mean there isn't any
positive potential even at closest distance of aminoacid from sheet. I
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
On 2/4/18 4:23 PM, Rose wrote:
Oooh, i mean roomMate :)))
Would you please answer my questions?
I already did. See my very detailed response below.
-Justin
Sent from my iPhone
On Feb 5, 2018, at 0:48, Rose wrote:
Sorry nothing mysterious,i'm rose(rose.rhmn93) in these all conversatio
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 my emails every
> times(i do
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 again
Sent from my iPhone
> On
I don't know whether you're intentionally changing your email address or
display name, but please refrain from doing so as it is very confusing
who I'm talking to.
On 2/4/18 4:00 PM, Nick Johans wrote:
maybe this is irrelative but i expeienced in pulling that when i decrease
dt from 2fs to 1
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 ,
On 2/4/18 3:25 PM, Rose wrote:
Jeah,i meant grompp :)))
and last question, i set constraint = h-Bonds, and dt=0.002 because Of
that(since usually h-Bonds have Max frequency and if i assume them
constraint so it's not reasonable to set dt=0.001 ) , is this assumption true?
You can alway
Jeah,i meant grompp :)))
and last question, i set constraint = h-Bonds, and dt=0.002 because Of
that(since usually h-Bonds have Max frequency and if i assume them
constraint so it's not reasonable to set dt=0.001 ) , is this assumption true?
Sent from my iPhone
> On Feb 4, 2018, at 23:30,
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
file)
The only reason to invoke grompp is if you're changing something about
the syste
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 10:44 AM, Rose wrote:
>
On 2/2/18 10:44 AM, Rose wrote:
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.
g_energy -f umbrella0.edr -o out.xvg
1 Bond
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,
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.
>>
g_energy -f umbrella0.edr -o out.xvg
>> 1 Bond
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.
g_energy -f umbrella0.edr -o out.xvg
1 Bond 2 Angle3 Proper-Dih. 4
Improper-Dih.
5 LJ-146 Coulomb-14
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
12:53 am (GMT+10:00)
To: gmx-us...@gromacs.org
Subject: [gmx-users] Umbrella sampling - Pull distance is larger than 0.49
times box size error
Hi,
I'm doing umbrella sampling and running into the above error. I can't
really increase the box size as that would make the system too big
Hi,
I'm doing umbrella sampling and running into the above error. I can't
really increase the box size as that would make the system too big nor can
I use pull-geometry = direction-periodic as I need to use NPT.
But I'm confused on why I get this error in the first place because my
periodic box i
On 1/18/18 12:37 AM, Moradzadeh, Alireza wrote:
Hi!
I am trying to do umbrella sampling between two 2D-sheets. I did it according
bevan lab tutorial the problem I encounter is that after pulling steps. I
perform umbrella sampling with rate of 0.0 however, two sheets get back
together and i
Hi!
I am trying to do umbrella sampling between two 2D-sheets. I did it according
bevan lab tutorial the problem I encounter is that after pulling steps. I
perform umbrella sampling with rate of 0.0 however, two sheets get back
together and initial configuration and final configuration are tot
Hi,
I'm trying to do an SMD simulation to generate configurations for Umbrella
sampling. I want to pull two groups together.
I'm having trouble understanding why the pulled distance must smaller than
the half the *shortest* box-vector length.
I know that distance is calculated taking periodicity
Oops,Sorrry. Sometimes big challenges make ones think hard and ignore
obvious issues.
Thank you so much Mr.justin and joao
On Sat, Jan 13, 2018 at 4:01 PM, João Henriques <
joao.m.a.henriq...@gmail.com> wrote:
> The output is very explicitly telling you what the problem is. You didn't
> provide a
The output is very explicitly telling you what the problem is. You didn'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
I'm relly sorry for asking you again and again but...
GROMACS: gmx distance, VERSION 5.1.4
Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Command line:
gmx distance -n index.ndx -f conf0.gro -select 'com of group 2 plus com
of group 6'
--
On 1/12/18 7:09 AM, rose rahmani wrote:
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
0.000
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 34 35 36 37 38 39 40 41 42 43 44
45..
[
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
Hi
Initially I followed US-gromacs tuitorial of Dr. Lemkul.it works very fine. so
I following the same tutorial for ligand-protein complex.
I have pulled the ligand over 300ps using following MD_pull.mdp and also
generated series of cordinate files (conf0.gro-conf300.gro) but problem is
[ 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
On 1/11/18 9:50 AM, rose rahmani wrote:
still like this
You're not using the command syntax shown in the link I provided.
-Justin
# This file was created Thu Jan 11 09:46:46 2018
# Created by:
# :-) GROMACS - gmx distance, VERSION 5.1.4 (-:
#
# Executable: /usr/local/grom
still like this
# This file was created Thu Jan 11 09:46:46 2018
# Created by:
# :-) GROMACS - gmx distance, VERSION 5.1.4 (-:
#
# Executable: /usr/local/gromacs/bin/gmx
# Data prefix: /usr/local/gromacs
# Command line:
# gmx distance -n index.ndx -f conf0.gro -oxyz dist0.xvg
On 1/11/18 3:43 AM, rose rahmani wrote:
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.for example; this my mdp
file for pulling:
integrator = md
dt = 0.001
nsteps
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.for example; this my mdp
file for pulling:
integrator = md
dt = 0.001
nsteps = 250
nstxout = 5000
n
On 1/4/18 2:48 AM, rose rahmani wrote:
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?
A COM distance of 0.3 nm is going to plac
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
-users@maillist.sys.kth.se
Subject: Re: [gmx-users] Umbrella sampling
- Message from Mark Abraham -
Date: Fri, 22 Dec 2017 00:42:31 +
From: Mark Abraham
Reply-To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Umbrella sampling
To: gmx-us...@gromacs.org
Cc
- Message from Mark Abraham -
Date: Fri, 22 Dec 2017 00:42:31 +
From: Mark Abraham
Reply-To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Umbrella sampling
To: gmx-us...@gromacs.org
Cc: gromacs.org_gmx-users@maillist.sys.kth.se
Hi,
Yes, the parsing of
- Message from "Jefferies D.F." -
Date: Tue, 19 Dec 2017 20:56:34 +
From: "Jefferies D.F."
Reply-To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Umbrella sampling
To: gmx-us...@gromacs.org,
gromacs.org_gmx-users@maillist.sys.kth.se
Out o
llist.sys.kth.se [
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of
> sp...@iacs.res.in [sp...@iacs.res.in]
> Sent: Tuesday, December 19, 2017 6:21 PM
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: Re: [gmx-users] Umbrella sampling
>
> - Messag
sys.kth.se
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of
sp...@iacs.res.in [sp...@iacs.res.in]
Sent: Tuesday, December 19, 2017 6:21 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] Umbrella sampling
- Message from Dhaniram Mahato -
Date: Tue, 1
- Message from Dhaniram Mahato -
Date: Tue, 19 Dec 2017 21:30:05 +0800
From: Dhaniram Mahato
Reply-To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Umbrella sampling
To: gmx-us...@gromacs.org
Hi,
There could be format problem. You can create your own .dat files
- Message from Dhaniram Mahato -
Date: Tue, 19 Dec 2017 21:30:05 +0800
From: Dhaniram Mahato
Reply-To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Umbrella sampling
To: gmx-us...@gromacs.org
Hi,
There could be format problem. You can create your own .dat files
Hi,
There could be format problem. You can create your own .dat files by typing
it. You have probably copied it from somewhere. I hope it will work then.
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-April/096839.html
Thanks
--
Gromacs Users mailing list
* Please search the
Hi all
I am doing umbrella sampling taking distance between COM as a reaction
coordinate. when I am trying to calculate PMF using the following command
gmx wham -it tpr-files.dat -if pullf-files.dat -o free.xvg -hist
hist.xvg
I got an error
Program: gmx wham, version 2016.3
Source file:
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 possible at all?1
> and
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? and what about time?is
4nS suitable for each window?
Thanks indeed
On Sat, Dec 16, 2017 at 10:05
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 -o pull.tpr
this is md_pull.mdp:
integrator = md
Hello,
I'm beginner in GROMACS. I'm trying to do umbrella sampling, but
profile.xvg file has nan value! i don't really know why this happens?
This is md_umbrella.mdp.
; Pull code
pull= umbrella
pull_ngroups= 1
pull_group0 = MX
pull_group1 =
On 12/4/17 1:33 AM, Sailesh Bataju wrote:
Hi,
I've started to pull a dimer of isobutane molecules as a production md
after npt equilibriation. Here is the md_pull.mdp file for production md.
; Umbrella pulling, production md
; preprocessing parameters
title = Umbrella Sampling
; run paramete
Hi,
I've started to pull a dimer of isobutane molecules as a production md
after npt equilibriation. Here is the md_pull.mdp file for production md.
; Umbrella pulling, production md
; preprocessing parameters
title = Umbrella Sampling
; run parameters
integrator = md ; leap-frog integrator for
On 12/3/17 8:01 AM, rose rahmani wrote:
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 example
conf13
On 12/3/17 8:42 AM, rose rahmani wrote:
I need to share you sth which just happened;
i run md_pull.mdp in two steps:
1--1nS( dt= 0.001 nsteps=100) ,
2--then i choosed last frame (conf1000.gro) and run it irst time for 2nS(
dt= 0.001 nsteps=200) and scond time for 4nS (dt=0.001 nstep
I need to share you sth which just happened;
i run md_pull.mdp in two steps:
1--1nS( dt= 0.001 nsteps=100) ,
2--then i choosed last frame (conf1000.gro) and run it irst time for 2nS(
dt= 0.001 nsteps=200) and scond time for 4nS (dt=0.001 nsteps=400)
and The protein was in normal shape
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 example
>> conf1300.gro amino acid was disi
On 11/29/17 2:45 PM, rose rahmani wrote:
Hello;
would you please send me Mr.lemkul's article link ? i can't find them.
It's linked here:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/01_pdb2gmx.html
If you need something regarding my published research, c
Hello;
would you please send me Mr.lemkul's article link ? i can't find them.
Thank you
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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 i choose ( by pull_coord1_dim) Z direction for pulling
On 11/28/17 10:00 AM, rose rahmani wrote:
Would "pull_geometry=periodic-distance" be another solution for it?
No. That affects how the reaction coordinate distance is calculated, not
the PBC treatment, which is intrinsic to any simulation using PBC.
-Justin
On Tue, Nov 28, 2017 at 5:11 P
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 normal shape
>> till almost conf1000.gro(and a
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 example
conf1300.gro amino acid was disintegrated. What does it mean? Would you
please help me?
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