Re: [gmx-users] WHAM

[rose rahmani]

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 very outdated Gromacs version.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= 2
 wall-atomtype= C C
 wall-type= 9-3
 wall-density = 150 150
 wall-ewald-zfac  = 3
 ewald-geometry   = 3dc
 fourierspacing   = 0.12
 tcoupl   = v-rescale
 tc-grps  = System
 tau-t= 0.1
 ref-t= 300
 ; Pull code
 pull= umbrella
 pull_ngroups= 1
 pull_group0 = ZnS
 pull_group1 = Protein
 pull_geometry   = direction
 pull_vec1   = 0 0 1
 pull_dim= N N Y
 pull_rate1  = -0.01
 pull_k1 = 5000
 pull_start  = yes
 pull_nstxout= 50

 then: mdrun -s pull.tpr
 then:trjconv -s 

Re: [gmx-users] my minimization structure looks like a messy box?

[Dilip H N]

Hello,
You need to use -pbc mol in your command for viewing the trajectory, then
this issue will be solved.



 Sent with Mailtrack


On Wed, Dec 13, 2017 at 11:23 PM, MD  wrote:

> ah, that explains. thanks Justin!
> Ming
>
> On Wed, Dec 13, 2017 at 11:42 AM, Justin Lemkul  wrote:
>
> >
> >
> > On 12/13/17 11:41 AM, MD wrote:
> >
> >> It looks like this
> >> https://drive.google.com/open?id=1DMy1otIYQZD8uxF6sZaZzZK4qN1z_qyD
> >>
> >
> > That's classic PBC.
> >
> > -Justin
> >
> >
> > On Wed, Dec 13, 2017 at 11:04 AM, Justin Lemkul  wrote:
> >>
> >>
> >>> On 12/13/17 11:02 AM, MD wrote:
> >>>
> >>> Hi Gromacs folks,
>  Any of you have experienced having a messy box looking gro file after
>  em.mdp?
> 
>  Probably http://www.gromacs.org/Documentation/Terminology/Periodic_
> >>> Boundary_Conditions but you'll have to define "messy" if that's not
> >>> what's going on.
> >>>
> >>> -Justin
> >>>
> >>> --
> >>> ==
> >>>
> >>> Justin A. Lemkul, Ph.D.
> >>> Assistant Professor
> >>> Virginia Tech Department of Biochemistry
> >>>
> >>> 303 Engel Hall
> >>> 340 West Campus Dr.
> >>> Blacksburg, VA 24061
> >>>
> >>> jalem...@vt.edu | (540) 231-3129
> >>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
> >>>
> >>> ==
> >>>
> >>> --
> >>> 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 visit
> >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >>> send a mail to gmx-users-requ...@gromacs.org.
> >>>
> >>>
> > --
> > ==
> >
> > Justin A. Lemkul, Ph.D.
> > Assistant Professor
> > Virginia Tech Department of Biochemistry
> >
> > 303 Engel Hall
> > 340 West Campus Dr.
> > Blacksburg, VA 24061
> >
> > jalem...@vt.edu | (540) 231-3129
> > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
> >
> > ==
> >
> > --
> > 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 visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> 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 visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>



-- 
With Best Regards,

DILIP.H.N
Ph.D Student
-- 
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 visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] set computer time on REMD simulation

[Qinghua Liao]

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!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] set computer time on REMD simulation

[YanhuaOuyang]

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!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] Measuring distance to the nearest image

[Anthony Nash]

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
-- 
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 visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Complication of errors, .itp file regarding

[RAHUL SURESH]

On Mon, 18 Dec 2017 at 1:27 AM, Justin Lemkul  wrote:

>
>
> On 12/17/17 2:54 PM, RAHUL SURESH wrote:
> > Dear all
> >
> > I managed to overcome above errors by manually creating an .itp file from
> > the parameter file of ffTK. But i end up with 139 warnings stating
> >
> >
> >
> >
> > *"Too few parameters on line (source file
> >
> /home/viji/Downloads/Gromacs/gromacs-2016.4/src/gromacs/gmxpreprocess/toppush.cpp,
> > line 1841) "*
> > Going through previous threads, the error arise because I have used atom
> > type instead of numbers in bond and angle section of .itp file. To change
> > all the names to number is really a difficult task ( though not
> impossible
> > ) and take lot ground work and much much time. I would like to know if
> > something can be done actually to create an itp through some script which
> > are already available, rather dumping all my time over this renumbering
> > process. Please sort out some better way.
> >
>
> Sounds like you have a totally broken topology. Solve the first issue
> you posted and to which I responded; it's much simpler to deal with.


Dear Justin

I got the first issue solved and this is what I get now. Broken topology..?
I have actually manually written it.  Is there any other option to generate
the itp file from parameter file of ffTK?



>
> -Justin
>
> >
> >
> > On Mon, 18 Dec 2017 at 12:41 AM, Justin Lemkul  wrote:
> >
> >>
> >> On 12/17/17 8:18 AM, RAHUL SURESH wrote:
> >>> Dear all
> >>>
> >>> Let me put forth the thing first. I have generated the parameter file
> >> using
> >>> fftk(structure.par) and derived the respective topology
> >> file(structure.top)
> >>> using topotools of vmd. Now to get the itp fiule, I manually copied the
> >>> necessary data from structure.top and made structure.itp file.
> >>>
> >>> For the command
> >>> * "gmx grompp -f em.mdp -c solv.gro -p alz.top -o ions.tpr"*
> >>>I get so many warning and errors.
> >>>
> >>> WARNING 1 [file THC.itp, line 3]:
> >>> Overriding atomtype CG2D1
> >>>
> >>> WARNING 31 [file THC.itp, line 37]:
> >>> Overriding Bond parameters.
> >>>
> >>> WARNING 35 [file THC.itp, line 111]:
> >>> Overriding U-B parameters.
> >>>
> >>> *69 warning messages*
> >>>
> >>> ERROR 1 [file THC.itp, line 158]:
> >>> Encountered a second block of parameters for dihedral type 9 for
> the
> >> same
> >>> atoms, with either different parameters and/or the first block has
> >>> multiple lines. This is not supported.
> >> The above errors are due to the fact that your molecule's .itp file
> >> includes parameters that are already part of the parent force field,
> >> hence grompp overrides them with the second instance. Don't do this. If
> >> an interaction is already specifically parametrized and is part of the
> >> force field, use it. Remove duplicated parameters from your .itp file.
> >>
> >>> *47 error messages*
> >>>
> >>> and finally
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> *Fatal error:number of coordinates in coordinate file (solv.gro,
> >>> 31285) does not match topology (alz.top, 31330)*
> >>> Please make it simple.
> >> The answer to this problem is always the same - incorrect bookkeeping.
> >> Check your work starting from addition of solvent and count how many of
> >> each species there are to make sure you've done things correctly.
> >>
> >> -Justin
> >>
> >> --
> >> ==
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Assistant Professor
> >> Virginia Tech Department of Biochemistry
> >>
> >> 303 Engel Hall
> >> 340 West Campus Dr.
> >> Blacksburg, VA 24061
> >>
> >> jalem...@vt.edu | (540) 231-3129
> >> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
> >>
> >> ==
> >>
> >> --
> >> 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 visit
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-requ...@gromacs.org.
> >>
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
> --
> 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 visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
*Regards,*
*Rahul 

Re: [gmx-users] WHAM

[Alex]

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    = 2
wall-atomtype    = C C
wall-type    = 9-3
wall-density = 150 150
wall-ewald-zfac  = 3
ewald-geometry   = 3dc
fourierspacing   = 0.12
tcoupl   = v-rescale
tc-grps  = System
tau-t    = 0.1
ref-t    = 300
; Pull code
pull    = umbrella
pull_ngroups    = 1
pull_group0 = ZnS
pull_group1 = Protein
pull_geometry   = direction
pull_vec1   = 0 0 1
pull_dim    = N N Y
pull_rate1  = -0.01
pull_k1 = 5000
pull_start  = yes
pull_nstxout    = 50

then: mdrun -s pull.tpr
then:trjconv -s pull.tpr -f traj_comp.xtc -o conf.gro -sep

i got 1000 configuration, i selected 27 of them and foe each of them 
i run md_umbrella.mdp


for example: grompp -f md_umbrella.mdp -c npt0.gro -t npt0.cpt -p 
topol.top -n index.ndx -o umbrella0.tpr and then:

mdrun -deffnm umbrella0 -pf pullf-umbrella0.xvg -px pullx-umbrella0.xvg

  .This is md_umbrella.mdp file:

ntegrator   = md
dt   = 0.002
nsteps   = 200
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    = 2
wall-atomtype    = C C
wall-type    = 9-3
wall-density = 150 150
wall-ewald-zfac  = 3
ewald-geometry   = 3dc
fourierspacing   = 0.12
tcoupl   = v-rescale
tc-grps  = System
tau-t    = 0.1
ref-t    = 300

pull    = umbrella

Re: [gmx-users] WHAM

[Justin Lemkul]

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= 2
wall-atomtype= C C
wall-type= 9-3
wall-density = 150 150
wall-ewald-zfac  = 3
ewald-geometry   = 3dc
fourierspacing   = 0.12
tcoupl   = v-rescale
tc-grps  = System
tau-t= 0.1
ref-t= 300
; Pull code
pull= umbrella
pull_ngroups= 1
pull_group0 = ZnS
pull_group1 = Protein
pull_geometry   = direction
pull_vec1   = 0 0 1
pull_dim= N N Y
pull_rate1  = -0.01
pull_k1 = 5000
pull_start  = yes
pull_nstxout= 50

then: mdrun -s pull.tpr
then:trjconv -s pull.tpr -f traj_comp.xtc -o conf.gro -sep

i got 1000 configuration, i selected 27 of them and foe each of them i run 
md_umbrella.mdp

for example: grompp -f md_umbrella.mdp -c npt0.gro -t npt0.cpt -p topol.top -n 
index.ndx -o umbrella0.tpr and then:
mdrun -deffnm umbrella0 -pf pullf-umbrella0.xvg -px pullx-umbrella0.xvg

  .This is md_umbrella.mdp file:

ntegrator   = md
dt   = 0.002
nsteps   = 200
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= 2
wall-atomtype= C C
wall-type= 9-3
wall-density = 150 150
wall-ewald-zfac  = 3
ewald-geometry   = 3dc
fourierspacing   = 0.12
tcoupl   = v-rescale
tc-grps  = System
tau-t= 0.1
ref-t= 300

pull= umbrella
pull_ngroups= 1
pull_group0 = ZnS
pull_group1 = Protein
pull_geometry   = direction
pull_vec1   = 0 0 1
pull_dim= N N Y
pull_rate1  = 0.0; 1 nm per  ns
pull_k1 = 5000
pull_start  = yes
pull_nstxout= 50
...

then i use :
wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal

i get histo.xvg and profile.xvg file but the profile.xvg contains nan vavlue. i 
don't know why?

# This file was created Wed Dec 13 14:54:35 2017
# by the following command:
# g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal
#
# g_wham is part of G R O M A C S:
#
# GROwing Monsters And Cloning Shrimps
#
@title "Umbrella potential"
@xaxis  label "z"
@yaxis  label "E (kcal mol\S-1\N)"
@TYPE xy
5.723834e-01-nan
6.714198e-01-nan
7.704562e-01-nan
8.694925e-01-nan

Re: [gmx-users] WHAM

[Rose]

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 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= 2
> wall-atomtype= C C
> wall-type= 9-3
> wall-density = 150 150
> wall-ewald-zfac  = 3
> ewald-geometry   = 3dc
> fourierspacing   = 0.12
> tcoupl   = v-rescale
> tc-grps  = System
> tau-t= 0.1
> ref-t= 300
> ; Pull code
> pull= umbrella
> pull_ngroups= 1
> pull_group0 = ZnS
> pull_group1 = Protein
> pull_geometry   = direction
> pull_vec1   = 0 0 1
> pull_dim= N N Y
> pull_rate1  = -0.01   
> pull_k1 = 5000
> pull_start  = yes
> pull_nstxout= 50
> 
> then: mdrun -s pull.tpr
> then:trjconv -s pull.tpr -f traj_comp.xtc -o conf.gro -sep
> 
> i got 1000 configuration, i selected 27 of them and foe each of them i run 
> md_umbrella.mdp
> 
> for example: grompp -f md_umbrella.mdp -c npt0.gro -t npt0.cpt -p topol.top 
> -n index.ndx -o umbrella0.tpr and then:
> mdrun -deffnm umbrella0 -pf pullf-umbrella0.xvg -px pullx-umbrella0.xvg
> 
>  .This is md_umbrella.mdp file:
> 
> ntegrator   = md
> dt   = 0.002
> nsteps   = 200
> 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= 2
> wall-atomtype= C C
> wall-type= 9-3
> wall-density = 150 150
> wall-ewald-zfac  = 3
> ewald-geometry   = 3dc
> fourierspacing   = 0.12
> tcoupl   = v-rescale
> tc-grps  = System
> tau-t= 0.1
> ref-t= 300
> 
> pull= umbrella
> pull_ngroups= 1
> pull_group0 = ZnS
> pull_group1 = Protein
> pull_geometry   = direction
> pull_vec1   = 0 0 1
> pull_dim= N N Y
> pull_rate1  = 0.0; 1 nm per  ns
> pull_k1 = 5000
> pull_start  = yes
> pull_nstxout= 50
> ...
> 
> then i use :
> wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal
> 
> i get histo.xvg and profile.xvg file but the profile.xvg contains nan vavlue. 
> i don't know why?
> 
> # This file was created Wed Dec 13 14:54:35 2017
> # by the following command:
> # g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal
> #
> # g_wham is part of G R O M A C S:
> #
> # GROwing Monsters And Cloning Shrimps
> #
> @title "Umbrella potential"
> @xaxis  label "z"
> @yaxis  label "E (kcal mol\S-1\N)"
> @TYPE xy
> 5.723834e-01-nan
> 6.714198e-01-nan
> 7.704562e-01-nan
> 8.694925e-01-nan
> 9.685289e-01-nan
> 1.067565e+00-nan
> 1.166602e+00-nan
> 1.265638e+00-nan 
> .
> .
> .
> .
> 
> Would 

Re: [gmx-users] WHAM

[Roja]

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 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= 2
> wall-atomtype= C C
> wall-type= 9-3
> wall-density = 150 150
> wall-ewald-zfac  = 3
> ewald-geometry   = 3dc
> fourierspacing   = 0.12
> tcoupl   = v-rescale
> tc-grps  = System
> tau-t= 0.1
> ref-t= 300
> 
> ; Pull code
> pull= umbrella
> pull_ngroups= 1
> pull_group0 = ZnS
> pull_group1 = Protein
> pull_geometry   = direction
> pull_vec1   = 0 0 1
> pull_dim= N N Y
> pull_rate1  = -0.01
> pull_k1 = 5000
> pull_start  = yes
> pull_nstxout= 50
> 
> then: mdrun -s pull.tpr
> then:trjconv -s pull.tpr -f traj_comp.xtc -o conf.gro -sep
> 
> i got 1000 configuration, i selected 27 of them and foe each of them i run
> md_umbrella.mdp
> 
> for example: grompp -f md_umbrella.mdp -c npt0.gro -t npt0.cpt -p topol.top
> -n index.ndx -o umbrella0.tpr and then:
> 
> mdrun -deffnm umbrella0 -pf pullf-umbrella0.xvg -px pullx-umbrella0.xvg
> 
> 
> .This is md_umbrella.mdp file:
> 
> ntegrator   = md
> dt   = 0.002
> nsteps   = 200
> 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= 2
> wall-atomtype= C C
> wall-type= 9-3
> wall-density = 150 150
> wall-ewald-zfac  = 3
> ewald-geometry   = 3dc
> fourierspacing   = 0.12
> tcoupl   = v-rescale
> tc-grps  = System
> tau-t= 0.1
> ref-t= 300
> 
> pull= umbrella
> pull_ngroups= 1
> pull_group0 = ZnS
> pull_group1 = Protein
> pull_geometry   = direction
> pull_vec1   = 0 0 1
> pull_dim= N N Y
> pull_rate1  = 0.0; 1 nm per  ns
> pull_k1 = 5000
> pull_start  = yes
> pull_nstxout= 50
> ...
> 
> then i use :
> 
> wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal
> 
> 
> i get histo.xvg and profile.xvg file but the profile.xvg contains nan
> vavlue. i don't know why?
> 
> 
> # This file was created Wed Dec 13 14:54:35 2017 # by the following
> command: # g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal
> # # g_wham is part of G R O M A C S: # # GROwing Monsters And Cloning
> Shrimps # @ title "Umbrella potential" @ xaxis label "z" @ yaxis label "E
> (kcal mol\S-1\N)" @TYPE xy 5.723834e-01 -nan 6.714198e-01 -nan 7.704562e-01
> -nan 8.694925e-01 -nan 9.685289e-01 -nan 1.067565e+00 -nan 1.166602e+00
> -nan 1.265638e+00 -nan
> 
> .
> 
> .
> 
> .
> 
> .
> 
> 
> Would you please help me? i have not 

Re: [gmx-users] Complication of errors, .itp file regarding

[Justin Lemkul]

On 12/17/17 2:54 PM, RAHUL SURESH wrote:

Dear all

I managed to overcome above errors by manually creating an .itp file from
the parameter file of ffTK. But i end up with 139 warnings stating




*"Too few parameters on line (source file
/home/viji/Downloads/Gromacs/gromacs-2016.4/src/gromacs/gmxpreprocess/toppush.cpp,
line 1841) "*
Going through previous threads, the error arise because I have used atom
type instead of numbers in bond and angle section of .itp file. To change
all the names to number is really a difficult task ( though not impossible
) and take lot ground work and much much time. I would like to know if
something can be done actually to create an itp through some script which
are already available, rather dumping all my time over this renumbering
process. Please sort out some better way.



Sounds like you have a totally broken topology. Solve the first issue 
you posted and to which I responded; it's much simpler to deal with.


-Justin




On Mon, 18 Dec 2017 at 12:41 AM, Justin Lemkul  wrote:



On 12/17/17 8:18 AM, RAHUL SURESH wrote:

Dear all

Let me put forth the thing first. I have generated the parameter file

using

fftk(structure.par) and derived the respective topology

file(structure.top)

using topotools of vmd. Now to get the itp fiule, I manually copied the
necessary data from structure.top and made structure.itp file.

For the command
* "gmx grompp -f em.mdp -c solv.gro -p alz.top -o ions.tpr"*
   I get so many warning and errors.

WARNING 1 [file THC.itp, line 3]:
Overriding atomtype CG2D1

WARNING 31 [file THC.itp, line 37]:
Overriding Bond parameters.

WARNING 35 [file THC.itp, line 111]:
Overriding U-B parameters.

*69 warning messages*

ERROR 1 [file THC.itp, line 158]:
Encountered a second block of parameters for dihedral type 9 for the

same

atoms, with either different parameters and/or the first block has
multiple lines. This is not supported.

The above errors are due to the fact that your molecule's .itp file
includes parameters that are already part of the parent force field,
hence grompp overrides them with the second instance. Don't do this. If
an interaction is already specifically parametrized and is part of the
force field, use it. Remove duplicated parameters from your .itp file.


*47 error messages*

and finally





*Fatal error:number of coordinates in coordinate file (solv.gro,
31285) does not match topology (alz.top, 31330)*
Please make it simple.

The answer to this problem is always the same - incorrect bookkeeping.
Check your work starting from addition of solvent and count how many of
each species there are to make sure you've done things correctly.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

--
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 visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-requ...@gromacs.org.



--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

--
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 visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Complication of errors, .itp file regarding

[RAHUL SURESH]

Dear all

I managed to overcome above errors by manually creating an .itp file from
the parameter file of ffTK. But i end up with 139 warnings stating




*"Too few parameters on line (source file
/home/viji/Downloads/Gromacs/gromacs-2016.4/src/gromacs/gmxpreprocess/toppush.cpp,
line 1841) "*
Going through previous threads, the error arise because I have used atom
type instead of numbers in bond and angle section of .itp file. To change
all the names to number is really a difficult task ( though not impossible
) and take lot ground work and much much time. I would like to know if
something can be done actually to create an itp through some script which
are already available, rather dumping all my time over this renumbering
process. Please sort out some better way.




On Mon, 18 Dec 2017 at 12:41 AM, Justin Lemkul  wrote:

>
>
> On 12/17/17 8:18 AM, RAHUL SURESH wrote:
> > Dear all
> >
> > Let me put forth the thing first. I have generated the parameter file
> using
> > fftk(structure.par) and derived the respective topology
> file(structure.top)
> > using topotools of vmd. Now to get the itp fiule, I manually copied the
> > necessary data from structure.top and made structure.itp file.
> >
> > For the command
> > * "gmx grompp -f em.mdp -c solv.gro -p alz.top -o ions.tpr"*
> >   I get so many warning and errors.
> >
> > WARNING 1 [file THC.itp, line 3]:
> >Overriding atomtype CG2D1
> >
> > WARNING 31 [file THC.itp, line 37]:
> >Overriding Bond parameters.
> >
> > WARNING 35 [file THC.itp, line 111]:
> >Overriding U-B parameters.
> >
> > *69 warning messages*
> >
> > ERROR 1 [file THC.itp, line 158]:
> >Encountered a second block of parameters for dihedral type 9 for the
> same
> >atoms, with either different parameters and/or the first block has
> >multiple lines. This is not supported.
>
> The above errors are due to the fact that your molecule's .itp file
> includes parameters that are already part of the parent force field,
> hence grompp overrides them with the second instance. Don't do this. If
> an interaction is already specifically parametrized and is part of the
> force field, use it. Remove duplicated parameters from your .itp file.
>
> > *47 error messages*
> >
> > and finally
> >
> >
> >
> >
> >
> > *Fatal error:number of coordinates in coordinate file (solv.gro,
> > 31285) does not match topology (alz.top, 31330)*
> > Please make it simple.
>
> The answer to this problem is always the same - incorrect bookkeeping.
> Check your work starting from addition of solvent and count how many of
> each species there are to make sure you've done things correctly.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
> --
> 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 visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
-- 
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 visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] The sum of the two largest charge group radii (X) is larger than rlist

[Faezeh Pousaneh]

Thanks Justin.
One component I mean system of only one type atom, each atom has two
charged virtual sites. So I can not see from VMD any breaking.


On Dec 17, 2017 8:10 PM, "Justin Lemkul"  wrote:



On 12/17/17 8:22 AM, Faezeh Pousaneh wrote:

> Dear Justin,
>
> How can I check that ''input configuration is "broken" across PBC'' ?
>  From vmd it is hard to say, since I only have one component system.
>

What is that one component? If a group of atoms is supposed to be in a
charge group, and it is split across the box, then you need to correct it
with trjconv or (if you are absolutely sure this isn't a problem) override
with grompp -maxwarn (dangerous and generally not wise).

-Justin



> Best regards
>
>
> On Fri, Dec 15, 2017 at 2:05 PM, Faezeh Pousaneh 
> wrote:
>
> The sum of the two largest charge group radii (7.984601) is larger than
>>rlist (0.347900).
>> the configuration looks fine across pbc. Everything looks normal.
>> Following is my md. I have user-specified potential so I need to have
>> cut-off values as given below.
>>
>>
>> integrator= md
>>   dt= 0.001
>>   nsteps= 300
>>   nstxout   = 10   ; save coordinates every 0
>> ps
>>   nstvout   = 10   ; save velocities every 0
>> ps
>>   nstlog= 10   ; update log file every
>>   nstenergy = 10; save energies every
>>   nstxtcout = 10   ; Output frequency for xtc file
>>   xtc-precision = 10   ; precision for xtc file
>>   ns_type   = grid; search neighboring grid cells
>>   nstlist   = 10   ;  fs
>>   pbc   = xyz ; 3-D PBC
>>   rlist = 0.3479  ; short-range neighborlist
>> cutoff
>> (in nm)
>>   rcoulomb  = 0.3479 ; short-range electrostatic
>> cutoff (in nm)
>>   rvdw = 0.3479; short-range van der Waals cutoff (in nm)
>>   coulombtype   = PME-user ; Particle Mesh Ewald for
>> long-range electrostatics
>>   pme_order = 4   ; cubic interpolation
>>   fourierspacing= 0.16; grid spacing for FFT
>>   vdw-type  = user
>>   Tcoupl= berendsen   ; modified Berendsen thermostat
>>   tc-grps   = co2   rest   ; two coupling groups -
>> more accurate
>>   tau_t =  0.1   0.1 ; time constant, in ps
>>   ref_t =  179.8  179.8 ; reference temperature, one
>> for each group, in K
>>   ;tc-grps  = system
>> cutoff-scheme  =group
>>   energygrps= co2 rest
>>   Pcoupl= no;Parrinello-Rahman
>>   Pcoupltype= Isotropic
>>   tau_p = 1.0
>>   compressibility   = 6.2e-5
>>   ref_p = 50.0
>>   gen_vel   = yes
>>   gen_temp  = 179.8
>>   gen_seed  = 712349
>>   DispCorr  =no;  EnerPres; account for cut-off vdW
>> scheme
>>   constraints   = all-bonds   ; all bonds constrained (fixed
>> length)
>>   continuation  = no ; Restarting after NPT
>>   constraint-algorithm  =  lincs   ; holonomic constraints
>>   lincs_iter= 1   ; accuracy of LINCS
>>   lincs_order   = 4   ; also related to accuracy
>>
>>
>>
>> Best regards
>>
>>
>> On Fri, Dec 15, 2017 at 1:44 PM, Justin Lemkul  wrote:
>>
>>
>>> On 12/15/17 4:26 AM, Faezeh Pousaneh wrote:
>>>
>>> Hi,

 I get this error only in NVT equlibration step, not in the NPT and
 production steps. Should I worry about it?

 In gromacs page it tell the error can come from 4 reasons, but how I can
 recognize which can be mine?

 Check the size of your largest charge group, value of rlist, or whether
>>> or not the input configuration is "broken" across PBC.
>>>
>>> -Justin
>>>
>>> http://www.gromacs.org/Documentation/Errors?highlight=docume
>>>
 ntation#The_sum_of_the_two_largest_charge_group_radii_(X)
 _is_larger_than.c2.a0rlist_-_rvdw.2frcoulomb

 Best regards

 --
>>> ==
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Assistant Professor
>>> Virginia Tech Department of Biochemistry
>>>
>>> 303 Engel Hall
>>> 340 West Campus Dr.
>>> Blacksburg, VA 24061
>>>
>>> jalem...@vt.edu | (540) 231-3129
>>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>>
>>> ==
>>>
>>> --
>>> 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 

Re: [gmx-users] Complication of errors, .itp file regarding

[Justin Lemkul]

On 12/17/17 8:18 AM, RAHUL SURESH wrote:

Dear all

Let me put forth the thing first. I have generated the parameter file using
fftk(structure.par) and derived the respective topology file(structure.top)
using topotools of vmd. Now to get the itp fiule, I manually copied the
necessary data from structure.top and made structure.itp file.

For the command
* "gmx grompp -f em.mdp -c solv.gro -p alz.top -o ions.tpr"*
  I get so many warning and errors.

WARNING 1 [file THC.itp, line 3]:
   Overriding atomtype CG2D1

WARNING 31 [file THC.itp, line 37]:
   Overriding Bond parameters.

WARNING 35 [file THC.itp, line 111]:
   Overriding U-B parameters.

*69 warning messages*

ERROR 1 [file THC.itp, line 158]:
   Encountered a second block of parameters for dihedral type 9 for the same
   atoms, with either different parameters and/or the first block has
   multiple lines. This is not supported.


The above errors are due to the fact that your molecule's .itp file 
includes parameters that are already part of the parent force field, 
hence grompp overrides them with the second instance. Don't do this. If 
an interaction is already specifically parametrized and is part of the 
force field, use it. Remove duplicated parameters from your .itp file.



*47 error messages*

and finally





*Fatal error:number of coordinates in coordinate file (solv.gro,
31285) does not match topology (alz.top, 31330)*
Please make it simple.


The answer to this problem is always the same - incorrect bookkeeping. 
Check your work starting from addition of solvent and count how many of 
each species there are to make sure you've done things correctly.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

--
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 visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] The sum of the two largest charge group radii (X) is larger than rlist

[Justin Lemkul]

On 12/17/17 8:22 AM, Faezeh Pousaneh wrote:

Dear Justin,

How can I check that ''input configuration is "broken" across PBC'' ?
 From vmd it is hard to say, since I only have one component system.


What is that one component? If a group of atoms is supposed to be in a 
charge group, and it is split across the box, then you need to correct 
it with trjconv or (if you are absolutely sure this isn't a problem) 
override with grompp -maxwarn (dangerous and generally not wise).


-Justin



Best regards


On Fri, Dec 15, 2017 at 2:05 PM, Faezeh Pousaneh 
wrote:


The sum of the two largest charge group radii (7.984601) is larger than
   rlist (0.347900).
the configuration looks fine across pbc. Everything looks normal.
Following is my md. I have user-specified potential so I need to have
cut-off values as given below.


integrator= md
  dt= 0.001
  nsteps= 300
  nstxout   = 10   ; save coordinates every 0 ps
  nstvout   = 10   ; save velocities every 0 ps
  nstlog= 10   ; update log file every
  nstenergy = 10; save energies every
  nstxtcout = 10   ; Output frequency for xtc file
  xtc-precision = 10   ; precision for xtc file
  ns_type   = grid; search neighboring grid cells
  nstlist   = 10   ;  fs
  pbc   = xyz ; 3-D PBC
  rlist = 0.3479  ; short-range neighborlist cutoff
(in nm)
  rcoulomb  = 0.3479 ; short-range electrostatic
cutoff (in nm)
  rvdw = 0.3479; short-range van der Waals cutoff (in nm)
  coulombtype   = PME-user ; Particle Mesh Ewald for
long-range electrostatics
  pme_order = 4   ; cubic interpolation
  fourierspacing= 0.16; grid spacing for FFT
  vdw-type  = user
  Tcoupl= berendsen   ; modified Berendsen thermostat
  tc-grps   = co2   rest   ; two coupling groups -
more accurate
  tau_t =  0.1   0.1 ; time constant, in ps
  ref_t =  179.8  179.8 ; reference temperature, one
for each group, in K
  ;tc-grps  = system
cutoff-scheme  =group
  energygrps= co2 rest
  Pcoupl= no;Parrinello-Rahman
  Pcoupltype= Isotropic
  tau_p = 1.0
  compressibility   = 6.2e-5
  ref_p = 50.0
  gen_vel   = yes
  gen_temp  = 179.8
  gen_seed  = 712349
  DispCorr  =no;  EnerPres; account for cut-off vdW
scheme
  constraints   = all-bonds   ; all bonds constrained (fixed
length)
  continuation  = no ; Restarting after NPT
  constraint-algorithm  =  lincs   ; holonomic constraints
  lincs_iter= 1   ; accuracy of LINCS
  lincs_order   = 4   ; also related to accuracy



Best regards


On Fri, Dec 15, 2017 at 1:44 PM, Justin Lemkul  wrote:



On 12/15/17 4:26 AM, Faezeh Pousaneh wrote:


Hi,

I get this error only in NVT equlibration step, not in the NPT and
production steps. Should I worry about it?

In gromacs page it tell the error can come from 4 reasons, but how I can
recognize which can be mine?


Check the size of your largest charge group, value of rlist, or whether
or not the input configuration is "broken" across PBC.

-Justin

http://www.gromacs.org/Documentation/Errors?highlight=docume

ntation#The_sum_of_the_two_largest_charge_group_radii_(X)
_is_larger_than.c2.a0rlist_-_rvdw.2frcoulomb

Best regards


--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

--
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 visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-requ...@gromacs.org.





--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

--
Gromacs Users mailing list

* Please search the archive 

Re: [gmx-users] Complication of errors, .itp file regarding

[RAHUL SURESH]

Dear all

I managed to overcome above errors by manually creating an .itp file from
the parameter file of ffTK. But i end up with 139 warnings stating




*"Too few parameters on line (source file
/home/viji/Downloads/Gromacs/gromacs-2016.4/src/gromacs/gmxpreprocess/toppush.cpp,
line 1841) "*
Going through previous threads, the error arise because I have used atom
type instead of numbers in bond and angle section of .itp file. To change
all the names to number is really a difficult task ( though not impossible
) and take lot ground work and much much time. I would like to know if
something can be done actually to create an itp through some script which
are already available, rather dumping all my time over this renumbering
process. Please sort out some better way.

On Sun, Dec 17, 2017 at 6:48 PM, RAHUL SURESH 
wrote:

> Dear all
>
> Let me put forth the thing first. I have generated the parameter file
> using fftk(structure.par) and derived the respective topology
> file(structure.top) using topotools of vmd. Now to get the itp fiule, I
> manually copied the necessary data from structure.top and made
> structure.itp file.
>
> For the command
> * "gmx grompp -f em.mdp -c solv.gro -p alz.top -o ions.tpr"*
>  I get so many warning and errors.
>
> WARNING 1 [file THC.itp, line 3]:
>   Overriding atomtype CG2D1
>
> WARNING 31 [file THC.itp, line 37]:
>   Overriding Bond parameters.
>
> WARNING 35 [file THC.itp, line 111]:
>   Overriding U-B parameters.
>
> *69 warning messages*
>
> ERROR 1 [file THC.itp, line 158]:
>   Encountered a second block of parameters for dihedral type 9 for the same
>   atoms, with either different parameters and/or the first block has
>   multiple lines. This is not supported.
>
> *47 error messages*
>
> and finally
>
>
>
>
>
> *Fatal error:number of coordinates in coordinate file (solv.gro,
> 31285) does not match topology (alz.top, 31330)*
> Please make it simple.
>
>
>
>
>
>
>
>
> --
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
>



-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
-- 
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 visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] WHAM

[rose rahmani]

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= 2
wall-atomtype= C C
wall-type= 9-3
wall-density = 150 150
wall-ewald-zfac  = 3
ewald-geometry   = 3dc
fourierspacing   = 0.12
tcoupl   = v-rescale
tc-grps  = System
tau-t= 0.1
ref-t= 300

; Pull code
pull= umbrella
pull_ngroups= 1
pull_group0 = ZnS
pull_group1 = Protein
pull_geometry   = direction
pull_vec1   = 0 0 1
pull_dim= N N Y
pull_rate1  = -0.01
pull_k1 = 5000
pull_start  = yes
pull_nstxout= 50

then: mdrun -s pull.tpr
then:trjconv -s pull.tpr -f traj_comp.xtc -o conf.gro -sep

i got 1000 configuration, i selected 27 of them and foe each of them i run
md_umbrella.mdp

for example: grompp -f md_umbrella.mdp -c npt0.gro -t npt0.cpt -p topol.top
-n index.ndx -o umbrella0.tpr and then:

mdrun -deffnm umbrella0 -pf pullf-umbrella0.xvg -px pullx-umbrella0.xvg


 .This is md_umbrella.mdp file:

ntegrator   = md
dt   = 0.002
nsteps   = 200
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= 2
wall-atomtype= C C
wall-type= 9-3
wall-density = 150 150
wall-ewald-zfac  = 3
ewald-geometry   = 3dc
fourierspacing   = 0.12
tcoupl   = v-rescale
tc-grps  = System
tau-t= 0.1
ref-t= 300

pull= umbrella
pull_ngroups= 1
pull_group0 = ZnS
pull_group1 = Protein
pull_geometry   = direction
pull_vec1   = 0 0 1
pull_dim= N N Y
pull_rate1  = 0.0; 1 nm per  ns
pull_k1 = 5000
pull_start  = yes
pull_nstxout= 50
...

then i use :

wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal


i get histo.xvg and profile.xvg file but the profile.xvg contains nan
vavlue. i don't know why?


# This file was created Wed Dec 13 14:54:35 2017 # by the following
command: # g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal
# # g_wham is part of G R O M A C S: # # GROwing Monsters And Cloning
Shrimps # @ title "Umbrella potential" @ xaxis label "z" @ yaxis label "E
(kcal mol\S-1\N)" @TYPE xy 5.723834e-01 -nan 6.714198e-01 -nan 7.704562e-01
-nan 8.694925e-01 -nan 9.685289e-01 -nan 1.067565e+00 -nan 1.166602e+00
-nan 1.265638e+00 -nan

.

.

.

.


Would you please help me? i have not encounter this problem before

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?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 

Re: [gmx-users] The sum of the two largest charge group radii (X) is larger than rlist

[Faezeh Pousaneh]

Dear Justin,

How can I check that ''input configuration is "broken" across PBC'' ?
>From vmd it is hard to say, since I only have one component system.


Best regards


On Fri, Dec 15, 2017 at 2:05 PM, Faezeh Pousaneh 
wrote:

>
> The sum of the two largest charge group radii (7.984601) is larger than
>   rlist (0.347900).
> the configuration looks fine across pbc. Everything looks normal.
> Following is my md. I have user-specified potential so I need to have
> cut-off values as given below.
>
>
> integrator= md
>  dt= 0.001
>  nsteps= 300
>  nstxout   = 10   ; save coordinates every 0 ps
>  nstvout   = 10   ; save velocities every 0 ps
>  nstlog= 10   ; update log file every
>  nstenergy = 10; save energies every
>  nstxtcout = 10   ; Output frequency for xtc file
>  xtc-precision = 10   ; precision for xtc file
>  ns_type   = grid; search neighboring grid cells
>  nstlist   = 10   ;  fs
>  pbc   = xyz ; 3-D PBC
>  rlist = 0.3479  ; short-range neighborlist cutoff
> (in nm)
>  rcoulomb  = 0.3479 ; short-range electrostatic
> cutoff (in nm)
>  rvdw = 0.3479; short-range van der Waals cutoff (in nm)
>  coulombtype   = PME-user ; Particle Mesh Ewald for
> long-range electrostatics
>  pme_order = 4   ; cubic interpolation
>  fourierspacing= 0.16; grid spacing for FFT
>  vdw-type  = user
>  Tcoupl= berendsen   ; modified Berendsen thermostat
>  tc-grps   = co2   rest   ; two coupling groups -
> more accurate
>  tau_t =  0.1   0.1 ; time constant, in ps
>  ref_t =  179.8  179.8 ; reference temperature, one
> for each group, in K
>  ;tc-grps  = system
> cutoff-scheme  =group
>  energygrps= co2 rest
>  Pcoupl= no;Parrinello-Rahman
>  Pcoupltype= Isotropic
>  tau_p = 1.0
>  compressibility   = 6.2e-5
>  ref_p = 50.0
>  gen_vel   = yes
>  gen_temp  = 179.8
>  gen_seed  = 712349
>  DispCorr  =no;  EnerPres; account for cut-off vdW
> scheme
>  constraints   = all-bonds   ; all bonds constrained (fixed
> length)
>  continuation  = no ; Restarting after NPT
>  constraint-algorithm  =  lincs   ; holonomic constraints
>  lincs_iter= 1   ; accuracy of LINCS
>  lincs_order   = 4   ; also related to accuracy
>
>
>
> Best regards
>
>
> On Fri, Dec 15, 2017 at 1:44 PM, Justin Lemkul  wrote:
>
>>
>>
>> On 12/15/17 4:26 AM, Faezeh Pousaneh wrote:
>>
>>> Hi,
>>>
>>> I get this error only in NVT equlibration step, not in the NPT and
>>> production steps. Should I worry about it?
>>>
>>> In gromacs page it tell the error can come from 4 reasons, but how I can
>>> recognize which can be mine?
>>>
>>
>> Check the size of your largest charge group, value of rlist, or whether
>> or not the input configuration is "broken" across PBC.
>>
>> -Justin
>>
>> http://www.gromacs.org/Documentation/Errors?highlight=docume
>>> ntation#The_sum_of_the_two_largest_charge_group_radii_(X)
>>> _is_larger_than.c2.a0rlist_-_rvdw.2frcoulomb
>>>
>>> Best regards
>>>
>>
>> --
>> ==
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalem...@vt.edu | (540) 231-3129
>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>
>> ==
>>
>> --
>> 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 visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>>
>
>
-- 
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 visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] Complication of errors, .itp file regarding

[RAHUL SURESH]

Dear all

Let me put forth the thing first. I have generated the parameter file using
fftk(structure.par) and derived the respective topology file(structure.top)
using topotools of vmd. Now to get the itp fiule, I manually copied the
necessary data from structure.top and made structure.itp file.

For the command
* "gmx grompp -f em.mdp -c solv.gro -p alz.top -o ions.tpr"*
 I get so many warning and errors.

WARNING 1 [file THC.itp, line 3]:
  Overriding atomtype CG2D1

WARNING 31 [file THC.itp, line 37]:
  Overriding Bond parameters.

WARNING 35 [file THC.itp, line 111]:
  Overriding U-B parameters.

*69 warning messages*

ERROR 1 [file THC.itp, line 158]:
  Encountered a second block of parameters for dihedral type 9 for the same
  atoms, with either different parameters and/or the first block has
  multiple lines. This is not supported.

*47 error messages*

and finally





*Fatal error:number of coordinates in coordinate file (solv.gro,
31285) does not match topology (alz.top, 31330)*
Please make it simple.








-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
-- 
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 visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.