Re: [gmx-users] PROTEIN FOLDING

[RAHUL SURESH]

On Tue, 19 Dec 2017 at 12:36 PM, Neha Gupta  wrote:

> Hi gromacs users,
>
> After MD simulation of protein-ligand complex for 5ns, can we view protein
> folding?
>
> How to do it?
>
> I want to ascertain if there is any conformation change in protein where
> the ligand binds. Is it possible?
>
> We observe hydrogen bonds through molecular docking. Hence, I want to make
> observation through MD simulation which is not obtained through docking.


You can perform Clustering analysis over particular PC sub space to measure
the structural changes.

>
>
> Can someone help me regarding this?
>
> Thank you very much in advance.
>
> Thanks,
> Neha
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*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
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Re: [gmx-users] PROTEIN FOLDING

[RAHUL SURESH]

On Tue, 19 Dec 2017 at 12:36 PM, Neha Gupta  wrote:

> Hi gromacs users,
>
> After MD simulation of protein-ligand complex for 5ns, can we view protein
> folding?


You can use various supporting tools from R language to debug your
trajectory but most third party software support NAMD and charmm format.
You can use VMD to convert the trajectory to dcd and use R language based
packages to read your trajectory

>
>
> How to do it?
>
> I want to ascertain if there is any conformation change in protein where
> the ligand binds. Is it possible?
>
> We observe hydrogen bonds through molecular docking. Hence, I want to make
> observation through MD simulation which is not obtained through docking.
>
> Can someone help me regarding this?
>
> Thank you very much in advance.
>
> Thanks,
> Neha
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
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> send a mail to gmx-users-requ...@gromacs.org.
>
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*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
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[gmx-users] GROMACS 2018 third beta release

[Mark Abraham]

Hi GROMACS users,

The third and final beta release of GROMACS 2018 is available! (We know
it's only 2017 right now, but by the time we make the real release it will
be almost 2018, so that seems like a good idea!) We'll issue a release
candidate shortly, and the final release very early in the new year, unless
any problems come to light.

We are making this available to you to get an early taste of how GROMACS
2018 will look and work, and most importantly to get feedback from you
about how well things work. While we try our hardest to keep the quality of
GROMACS as high as possible, we’re human, we overlook things while doing
other things, and we need your many pairs of eyes to help build a tool that
we can all use to do good science! We really need you to test your kinds of
simulation on your hardware, both for correctness and performance. This is
particularly important if you are using "interesting" hardware or
compilers, because we can't test all of them!

We've fixed a number of minor issues that users and developers identified -
please do try out the new version to see if you agree that things have been
fixed where we think they have. No major issues have been identified, which
is very good news. See the release notes for details.

Please do not use this version for doing science you plan to publish - it
needs more testing before it’s reliable enough for that. Similarly, please
don’t use this version as a base for a project that bundles or forks
GROMACS.

What new things can you expect? (See the release notes for more details.)
* support for PME running on a GPU
* improvements for performance of the short-ranged scheme, particularly on
GPUs, through optimizing the pair-list handling
* support for the AWH adaptive biasing scheme
* new simulation quality checks on physical properties of the integrator
* CPU-side enhancements from adding some or better SIMD support to several
computations
* more reporting of conserved quantities for integrators

Just so you know, a fair bit of the work done since 2016 has been
re-organizational, rather than new features or faster performance.

There’s lots of other new things, and a few old things removed - please see
the link to the release notes. All the content of GROMACS 2016.4 (plus
several yet-to-be-released bug fixes) is present, apart from features that
have been removed.

If all goes to plan, we hope to ship the final 2018 release in time for the
New Year, but that relies on people joining in and helping us test! We hope
you will consider making that contribution, so that we can continue to
deliver high-quality free simulation software that will be useful to you on
January 1.

You can find the code, manual, release notes, installation instructions and
testsuite at the links below.

Code: ftp://ftp.gromacs.org/pub/gromacs/gromacs-2018-beta3.tar.gz
Documentation: http://manual.gromacs.org/documentation/2018-beta3/index.html
(includes install guide, user guide, reference manual)
Release Notes:
http://manual.gromacs.org/documentation/2018-beta3/ReleaseNotes/index.html
Test Suite:
http://gerrit.gromacs.org/download/regressiontests-2018-beta3.tar.gz

Happy testing!

Mark Abraham
GROMACS development manager
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Re: [gmx-users] PROTEIN FOLDING

[Nikhil Maroli]

After MD simulation of protein-ligand complex for 5ns, can we view protein
folding?

mostly, NO

Search what time range 'protein folding' is happening.

How to do it?

I want to ascertain if there is any conformation change in protein where
the ligand binds. Is it possible?


You might want to do PCA, RMSD and DSSP

We observe hydrogen bonds through molecular docking. Hence, I want to make
observation through MD simulation which is not obtained through docking.


gmx hbond

Can someone help me regarding this?


i really wondering what is possible in 5 ns simulation time, you may
try to extend it up to 100 ns or atleast a 50 ns.

Thank you very much in advance.
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[gmx-users] PROTEIN FOLDING

[Neha Gupta]

Hi gromacs users,

After MD simulation of protein-ligand complex for 5ns, can we view protein
folding?

How to do it?

I want to ascertain if there is any conformation change in protein where
the ligand binds. Is it possible?

We observe hydrogen bonds through molecular docking. Hence, I want to make
observation through MD simulation which is not obtained through docking.

Can someone help me regarding this?

Thank you very much in advance.

Thanks,
Neha
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Re: [gmx-users] Measuring distance to the nearest image

[Anthony Nash]

Just wondering whether anyone has had any luck with a similar problem? If not, 
I’ll knock a script together and make it available. I was hoping not to 
reinvent the wheel if there was already a way. 

Regards
Anthony

On 18/12/2017 06:23, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on 
behalf of Anthony Nash"  wrote:


Hi all,

I am trying to measure the distance between the COM of two side chain 
functional groups across the periodic boundary to their nearest image rather 
than across the unit cell itself. I have tried several gromacs distance 
commands with no success and more at random as I trawl through the help and 
manual, so I won’t replicate those commands here.

This link is a hand drawn image of what I am trying to do. I would like to 
measure how far apart the two large dots are across the periodic boundary. VMD 
gives me roughly 1 nm, but the Gromacs commands give me 8 nm as it takes the 
measurement from within the unit cell.


https://www.researchgate.net/profile/Anthony_Nash3/post/How_to_calculate_distance_between_groups_into_the_nearest_image_using_Gromacs/attachment/5a30d10eb53d2f0bba43e5c3/AS:571001131417600@1513148686095/image/IMG_20171213_065534.jpg
If this involve a tcl script in VMD I would appreciate knowing how to code 
for an atom selection in a “Periodic” image rather than the “Self”.

Loads of thanks!
Anthony
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[gmx-users] g_mindsit contact analysis

[soumadwip ghosh]

Hi all,

I have simulated a duplex RNA in presence of a CNT in aqueous medium. The
gromacs version I used was 4.5.6. The two species were kept 2 nm apart to
begin with. I wanted to calculate how many RNA atoms were within 4 angstrom
distance from the CNT on a per-frame trajectory basis. I used the following
command:
 g_mindist -f md.xtc -s md.tpr -d 0.4 -n index.ndx -on nc.xvg

The CNT is composed of 1500 atoms while the nucleic acid is 370. The
contacts I am getting as a function of time is ~2000. Why is the value so
large? I did not specify COM or any particular atom belonging to CNT in my
index file and when prompted I selected the entire CNT and RNA for
g_mindist analysis. Is the number large because it calculates all the
atomic contacts between the two structures and prints it in the .xvg file?
For example, at 100 ps if each carbon atom  is having at least two RNA
contacts then the total contacts will be 3000. Is it being calculated this
way or something else is going on?

Thank you for your answer in advance

Soumadwip Ghosh
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[gmx-users] Free energy perturbation - table extension and blowing system

[Krzysztof Makuch]

Hi,
I want to calculate 'solvation' energy of lutein in bilayer and water by
Free Energy Perturbation. When I'm running a normal MD, or some kind of
steering dynamics,my system works just fine. After addition of FEP
parameters, em runs, but instantly  returns series of warnings:

WARNING: Listed nonbonded interaction between particles 6461 and 6482
at distance 2.545 which is larger than the table limit 2.200 nm.

This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several interactions.

IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason.

The same thing repeats for several pairs of atoms, only in one
transmembrane molecule. As I said, everything is fine without FEP
parameters. For this instance I'm using the following parameters adapted
stright from the Bevanlab tutorial:

; Run control
integrator   = steep
nsteps   = 5000
; EM criteria and other stuff
emtol= 100
emstep   = 0.01
niter= 20
nbfgscorr= 10
; Output control
nstlog   = 1
nstenergy= 1
; Neighborsearching and short-range nonbonded interactions
cutoff-scheme= verlet
nstlist  = 1
ns_type  = grid
pbc  = xyz
rlist= 1.2
; Electrostatics
coulombtype  = PME
rcoulomb = 1.2
; van der Waals
vdwtype  = cutoff
vdw-modifier = potential-switch
rvdw-switch  = 1.0
rvdw = 1.2
; Apply long range dispersion corrections for Energy and Pressure
DispCorr  = EnerPres
; Spacing for the PME/PPPM FFT grid
fourierspacing   = 0.12
; EWALD/PME/PPPM parameters
pme_order= 6
ewald_rtol   = 1e-06
epsilon_surface  = 0
; Temperature and pressure coupling are off during EM
tcoupl   = no
pcoupl   = no
; Free energy control stuff
free_energy  = yes
init_lambda_state= 0
delta_lambda = 0
calc_lambda_neighbors= 1
; Vectors of lambda specified here
; Each combination is an index that is retrieved from init_lambda_state for
each simulation
; init_lambda_state012345678
910   11   12   13   14   15   16   17   18   19   20
vdw_lambdas  = 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40
0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00
coul_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
; We are not transforming any bonded or restrained interactions
bonded_lambdas   = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
restraint_lambdas= 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
; Masses are not changing (particle identities are the same at lambda = 0
and lambda = 1)
mass_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
; Not doing simulated temperting here
temperature_lambdas  = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
; Options for the decoupling
sc-alpha = 0.5
sc-coul  = no
sc-power = 1.0
sc-sigma = 0.3
couple-moltype   = lutein
couple-lambda0   = vdw
couple-lambda1   = none
couple-intramol  = no
nstdhdl  = 10
; No velocities during EM
gen_vel  = no
; options for bonds
constraints  = h-bonds
; Type of constraint algorithm
constraint-algorithm = lincs
; Do not constrain the starting configuration
continuation = no
; Highest order in the expansion of the constraint coupling matrix
lincs-order  = 12


What I've tried by now and didn't work:
- I've tried to increase table extension, but it didn't do any good.
- I've tried to change the charge groups, which are now 1 atom = 1 group
for this molecule
- I was trying to solve this with gromacs 4, 5 and 16'. Warnings were
similar.
If I try to run further FEP steps the system with FEP parameters blows up.
MD without FEP simulates doesn't cause any problems.
My guess is I'm missing something inside FEP parameters. I'm using GROMACS
for several years by now and for the first time I can't solve the problem
by myself. 

Re: [gmx-users] GROMACS 2018 second beta

[Ali Ahmed]

Dear Mark,
Thank you for all of your efforts.
I wish you added an option for applying external magnetic field in this
version.
Thanks
Ali

On Mon, Dec 11, 2017 at 8:54 PM, Mark Abraham 
wrote:

> Hi GROMACS users,
>
> The second beta release of GROMACS 2018 is available! (We know it's only
> 2017 right now, but by the time we make the real release it will be almost
> 2018, so that seems like a good idea!)
>
> We are making this available to you to get an early taste of how GROMACS
> 2018 will look and work, and most importantly to get feedback from you
> about how well things work. While we try our hardest to keep the quality of
> GROMACS as high as possible, we’re human, we overlook things while doing
> other things, and we need your many pairs of eyes to help build a tool that
> we can all use to do good science! We really need you to test your kinds of
> simulation on your hardware, both for correctness and performance. This is
> particularly important if you are using "interesting" hardware or
> compilers, because we can't test all of them!
>
> We've fixed a number of minor issues that users and developers identified -
> please do try out the new version to see if you agree that things have been
> fixed where we think they have. No major issues have been identified, which
> is very good news. See the release notes for details.
>
> Please do not use this version for doing science you plan to publish - it
> needs more testing before it’s reliable enough for that. Similarly, please
> don’t use this version as a base for a project that bundles or forks
> GROMACS.
>
> What new things can you expect? (See the release notes for more details.)
> * support for PME running on a GPU
> * improvements for performance of the short-ranged scheme, particularly on
> GPUs, through optimizing the pair-list handling
> * support for the AWH adaptive biasing scheme
> * new simulation quality checks on physical properties of the integrator
> * CPU-side enhancements from adding some or better SIMD support to several
> computations
> * more reporting of conserved quantities for integrators
>
> Just so you know, a fair bit of the work done since 2016 has been
> re-organizational, rather than new features or faster performance.
>
> There’s lots of other new things, and a few old things removed - please see
> the link to the release notes. All the content of GROMACS 2016.4 (plus
> several yet-to-be-released bug fixes) is present, apart from features that
> have been removed.
>
> If all goes to plan, we hope to ship the final 2018 release in time for the
> New Year, but that relies on people joining in and helping us test! We hope
> you will consider making that contribution, so that we can continue to
> deliver high-quality free simulation software that will be useful to you on
> January 1.
>
> You can find the code, manual, release notes, installation instructions and
> testsuite at the links below.
>
> Code: ftp://ftp.gromacs.org/pub/gromacs/gromacs-2018-beta2.tar.gz
> Documentation: http://manual.gromacs.org/documentation/2018-beta2/
> index.html
> (includes install guide, user guide, reference manual)
> Release Notes:
> http://manual.gromacs.org/documentation/2018-beta2/ReleaseNotes/index.html
> Test Suite:
> http://gerrit.gromacs.org/download/regressiontests-2018-beta2.tar.gz
>
> Happy testing!
>
> Mark Abraham
> GROMACS Development Manager
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
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>
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> send a mail to gmx-users-requ...@gromacs.org.
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[gmx-users] PME computation for triclinic box

[Mariia Savenko]

Good morning,
I'd like to ask how PME computations for triclinic box are done in Gromacs.
I'd like to compute electric field for my triclinic box and I'm not sure
that I understand correctly how it's done in Gromacs.
Sincerely,
Mariia
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Re: [gmx-users] WHAM

[Rose]

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

> On Dec 18, 2017, at 11:58, Alex  wrote:
> 
>> On 12/18/2017 1:14 AM, João Henriques wrote:
>> First, you don't need "special computers" to run or compile gromacs. It
>> helps to have multiple compute nodes at your disposal, but it isn't a
>> requirement *per se*. Also, you don't need to be root to compile your own
>> gromacs installation. You can indeed install your own gromacs version on
>> the cluster you use to run your simulations.
> Well, I do need "special computers" to run GMX. :)
> Jokes aside, this is a solid point -- even if one uses a Windows machine, 
> virtualbox+linux+gromacs is always useful to tinker at home for when you have 
> no access to the "special computer." That, or cygwin, although that thing 
> nauseates me.
> 
> Rose, if you are a student, it would be a good idea to ask for better 
> instruction from your professors. This board is quite limited in replacing 
> the kind of instruction you may need. Three months is actually a reasonable 
> amount of time to get the basics of MD and Gromacs right. Without those 
> basics, it is completely pointless to try doing any work.
> 
> Alex
> 
> 
>> 
>>> On Mon, Dec 18, 2017 at 8:57 AM, rose rahmani  wrote:
>>> 
>>> Dear Justin,I don't have special computers to be compatible with these
>>> softwares and run complex calculations.So i have to connect to some
>>> computers which is not mine and the old version is installed there.i can't
>>> update them because i'm just a normal user and not a root one! So there are
>>> two choices; not using GROMACS at all OR be convinced with the old
>>> versions. i choose latter!
>>> WHO don't like an upgraded software sir?! you are not talking with a
>>> headstrong person ;) i like to use V.2018 but it's not possible for me, i
>>> hope you understand me.Just this!
>>> You are talking with 3 months experienced student without any experience in
>>> any similar simulation software before!
>>> 
>>> I agree with you Alex he is a modest person ;)
>>> I understand sometimes it's not possible to say what the problem exactly
>>> is, but i ask to know if you had these problems before how did you 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, 2017 at 12:52 AM, Alex  wrote:
 
 Rose,
 
 Although in my opinion Justin does know everything, the problem is with
 your question. You've posted the same thing over and over (and over), and
 noone replied -- this could be an indicator that people simply have
>>> nothing
 to say. We don't know anything about your system, we don't know whether
>>> it
 is stable, what is its dynamics, etc, etc. On top of this, you are using
>>> a
 very outdated Gromacs version.
 
 From my own experience with all versions above 5.0.x, pull in Gromacs
>>> does
 work well, as long as your system behaves as expected without pulling,
>>> and,
 once that has been confirmed, you use a properly selected set of pull
 parameters. There are basic procedures for checking your system _prior
>>> to_
 production simulations involving external stimuli (fields, pulling, etc)
>>> --
 please follow them. And please, Please be mindful of what this message
 board is, and especially of what it is not.
 
 Good luck!
 
 Alex
 
 
 
> On 12/17/2017 1:44 PM, Justin Lemkul wrote:
> 
> 
>> On 12/17/17 3:39 PM, Rose wrote:
>> 
>> Why you don't answer me?is there anything wrong in my question?
> Contrary to popular opinion, I don't know everything :) If I don't reply
> to a question, it is because I have nothing useful to contribute.
> 
> But since you asked, diagnosing what appears to be buggy behavior in
> wildly outdated (and unsupported, as I warned you) versions of the code
>>> is
> not a wise use of time. Upgrade to the latest version and try again.
> 
> -Justin
> 
> 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 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

Re: [gmx-users] WHAM

[Alex]

On 12/18/2017 1:14 AM, João Henriques wrote:

First, you don't need "special computers" to run or compile gromacs. It
helps to have multiple compute nodes at your disposal, but it isn't a
requirement *per se*. Also, you don't need to be root to compile your own
gromacs installation. You can indeed install your own gromacs version on
the cluster you use to run your simulations.

Well, I do need "special computers" to run GMX. :)
Jokes aside, this is a solid point -- even if one uses a Windows 
machine, virtualbox+linux+gromacs is always useful to tinker at home for 
when you have no access to the "special computer." That, or cygwin, 
although that thing nauseates me.


Rose, if you are a student, it would be a good idea to ask for better 
instruction from your professors. This board is quite limited in 
replacing the kind of instruction you may need. Three months is actually 
a reasonable amount of time to get the basics of MD and Gromacs right. 
Without those basics, it is completely pointless to try doing any work.


Alex




On Mon, Dec 18, 2017 at 8:57 AM, rose rahmani  wrote:


Dear Justin,I don't have special computers to be compatible with these
softwares and run complex calculations.So i have to connect to some
computers which is not mine and the old version is installed there.i can't
update them because i'm just a normal user and not a root one! So there are
two choices; not using GROMACS at all OR be convinced with the old
versions. i choose latter!
WHO don't like an upgraded software sir?! you are not talking with a
headstrong person ;) i like to use V.2018 but it's not possible for me, i
hope you understand me.Just this!
You are talking with 3 months experienced student without any experience in
any similar simulation software before!

I agree with you Alex he is a modest person ;)
I understand sometimes it's not possible to say what the problem exactly
is, but i ask to know if you had these problems before how did you 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, 2017 at 12:52 AM, Alex  wrote:


Rose,

Although in my opinion Justin does know everything, the problem is with
your question. You've posted the same thing over and over (and over), and
noone replied -- this could be an indicator that people simply have

nothing

to say. We don't know anything about your system, we don't know whether

it

is stable, what is its dynamics, etc, etc. On top of this, you are using

a

very outdated Gromacs version.

 From my own experience with all versions above 5.0.x, pull in Gromacs

does

work well, as long as your system behaves as expected without pulling,

and,

once that has been confirmed, you use a properly selected set of pull
parameters. There are basic procedures for checking your system _prior

to_

production simulations involving external stimuli (fields, pulling, etc)

--

please follow them. And please, Please be mindful of what this message
board is, and especially of what it is not.

Good luck!

Alex



On 12/17/2017 1:44 PM, Justin Lemkul wrote:



On 12/17/17 3:39 PM, Rose wrote:


Why you don't answer me?is there anything wrong in my question?


Contrary to popular opinion, I don't know everything :) If I don't reply
to a question, it is because I have nothing useful to contribute.

But since you asked, diagnosing what appears to be buggy behavior in
wildly outdated (and unsupported, as I warned you) versions of the code

is

not a wise use of time. Upgrade to the latest version and try again.

-Justin

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 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
dt   = 0.002
nsteps   = 100
nstxout  = 5000
nstvout  = 5000
nstfout  = 500
nstlog   = 500
nstenergy= 1000
nstxtcout= 1000
nstlist  = 10
rlist= 1.5
coulombtype  = pme
rcoulomb = 1.5
vdwtype  = Switch
rvdw_switch  = 1.0
rvdw = 1.2
pcoupl   = no
gen_vel  = no
constraints  = h-bonds
ns_type  = grid
pbc  = xy
freezegrps   = WAL ZnS
freezedim= Y Y Y Y Y Y
energygrp-excl   = WAL WAL ZnS ZnS
energygrps   = SOL WAL ZnS Protein NA CL
nwall 

Re: [gmx-users] WHAM

[João Henriques]

This has nothing to do with your initial question, but I there are a few
misconceptions in your last email that you should be aware of.

First, you don't need "special computers" to run or compile gromacs. It
helps to have multiple compute nodes at your disposal, but it isn't a
requirement *per se*. Also, you don't need to be root to compile your own
gromacs installation. You can indeed install your own gromacs version on
the cluster you use to run your simulations.

Finally, version 2018 is still a beta testing version, so it's probably not
a good idea to use it until it's released as a stable version.

P.S.: Justin does a lot more than the average mortal, specially when it
comes to MD simulations and Gromacs. However, no one ever knows everything.

Cheers,

J

On Mon, Dec 18, 2017 at 8:57 AM, rose rahmani  wrote:

> Dear Justin,I don't have special computers to be compatible with these
> softwares and run complex calculations.So i have to connect to some
> computers which is not mine and the old version is installed there.i can't
> update them because i'm just a normal user and not a root one! So there are
> two choices; not using GROMACS at all OR be convinced with the old
> versions. i choose latter!
> WHO don't like an upgraded software sir?! you are not talking with a
> headstrong person ;) i like to use V.2018 but it's not possible for me, i
> hope you understand me.Just this!
> You are talking with 3 months experienced student without any experience in
> any similar simulation software before!
>
> I agree with you Alex he is a modest person ;)
> I understand sometimes it's not possible to say what the problem exactly
> is, but i ask to know if you had these problems before how did you 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, 2017 at 12:52 AM, Alex  wrote:
>
> > Rose,
> >
> > Although in my opinion Justin does know everything, the problem is with
> > your question. You've posted the same thing over and over (and over), and
> > noone replied -- this could be an indicator that people simply have
> nothing
> > to say. We don't know anything about your system, we don't know whether
> it
> > is stable, what is its dynamics, etc, etc. On top of this, you are using
> a
> > very outdated Gromacs version.
> >
> > From my own experience with all versions above 5.0.x, pull in Gromacs
> does
> > work well, as long as your system behaves as expected without pulling,
> and,
> > once that has been confirmed, you use a properly selected set of pull
> > parameters. There are basic procedures for checking your system _prior
> to_
> > production simulations involving external stimuli (fields, pulling, etc)
> --
> > please follow them. And please, Please be mindful of what this message
> > board is, and especially of what it is not.
> >
> > Good luck!
> >
> > Alex
> >
> >
> >
> > On 12/17/2017 1:44 PM, Justin Lemkul wrote:
> >
> >>
> >>
> >> On 12/17/17 3:39 PM, Rose wrote:
> >>
> >>> Why you don't answer me?is there anything wrong in my question?
> >>>
> >>
> >> Contrary to popular opinion, I don't know everything :) If I don't reply
> >> to a question, it is because I have nothing useful to contribute.
> >>
> >> But since you asked, diagnosing what appears to be buggy behavior in
> >> wildly outdated (and unsupported, as I warned you) versions of the code
> is
> >> not a wise use of time. Upgrade to the latest version and try again.
> >>
> >> -Justin
> >>
> >> 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 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
>  dt   = 0.002
>  nsteps   = 100
>  nstxout  = 5000
>  nstvout  = 5000
>  nstfout  = 500
>  nstlog   = 500
>  nstenergy= 1000
>  nstxtcout= 1000
>  nstlist  = 10
>  rlist= 1.5
>  coulombtype  = pme
>  rcoulomb = 1.5
>  vdwtype  = Switch
>  rvdw_switch  = 1.0
>  rvdw = 1.2
>  pcoupl   = no
>  gen_vel  = no
>  constraints  = h-bonds
>  ns_type  = grid
>  pbc  = xy
>  

[gmx-users] Grompp error : Incorrect number of parameters

[RAHUL SURESH]

Dear all

For grompp em.mdp I get an error

ERROR 1 [file THC.itp, line 89]:
  Incorrect number of parameters - found 2, expected 4 or 8 for U-B.

My itp file as follows

[ angles ]

1   2   29   579.178   109.588 *{Line 89}*
1   2   3 532.192   112.817
2   3   31   551.424   109.189

>From the manual chapter 5, function of U-B is 5. And it works fine for
function type 2 and 8.

Any thing better could be done?

*PS: The itp file is constructed from parameter file of ffTK.*

Thank you


-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
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Re: [gmx-users] set computer time on REMD simulation

[YanhuaOuyang]

Sorry, it seems that I did not express my problem clearly.
I add "-maxh 0.1", it should be terminated until 10 minutes maximumly. However, 
the MD did not stop after over one hour.








At 2017-12-18 15:48:10, "Qinghua Liao"  wrote:
>Hello,
>
>If I understand correctly, it terminates at 0.99*t, t is the time you 
>set in hour.
>In you case, you simulation should be terminated at 0.1*0.99 = 0.099 h, 
>which is 5.94 minutes.
>
>PS: 0.1 h is not 10 minutes, but 6 minutes.
>
>All the best,
>Qinghua
>
>On 12/18/2017 08:05 AM, YanhuaOuyang wrote:
>> Dear gromacs user,
>>  The computing workstation I used has a limited time: 6 hours, 
>> namely the  REMD will be terminated after 6 hours. So I add option "-maxh 
>> 0.1" in the MD commands to test. The md commands are  as below:
>>   mdrun_mpi  -s remd_.tpr -multi 20 -replex 1000  -x remd_.xtc -cpo 
>> remd_.cpt -e remd_.edr -g remd_.log -c remd_.gro -maxh 0.1
>>
>> However the REMD did not terminate after the test time, 10 minutes.
>> Why the option "-maxh 0.1" did not work?
>> How to solve the limited time problem?
>>
>> Ouyang,
>> Best regards
>
>-- 
>Gromacs Users mailing list
>
>* Please search the archive at 
>http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
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