Re: [gmx-users] Can you please tell me the exact command? Re: Restart a stopped simulation after a power failure? : Not working in Gromacs 5.1.4

[Anshul Lahariya]

Hlw

Plzz use

gmx mdrun -v -deffnm md_0_1 -cpi md_0_1.cpt

On 18 May 2017 9:01 p.m., "Adarsh V. K." 
wrote:

> Dear Dr. Mark,
>
> Thank you for the prompt reply. I have been struggling with the issue for
> couple month time. Would you please advise me how to use  " -deffnm " flag
> in commands?
>
> # gmx mdrun  -s  md_0_1.tpr  -cpi  md_0_1_prev.cpt  -v  -deffnm
>
> Will the above command will successful restart a stopped simulation and
> append?, If no could you please type the exact command I should use to
> solve the issue.
>
> Sincerely,
>
> Adarsh V. K.
> Research Scholar (PhD)
> National Institute of Technology, Calicut ( NIT C )
> Kerala state, India
>
> --
> On Thu, May 18, 2017 at 7:13 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > Some of your commands and outputs are inconsistent. You can't get
> > md_0_1.log without e.g. using -deffnm, and you'll only get md.log if you
> > don't use deffnm. But if you change that when trying to do your
> > continuation, mdrun won't know how to append because you haven't told it
> > that the old name. Be consistent. Your whole trajectory is present in all
> > your output files, but you're going to have to concatenate them yourself,
> > e.g. with gmx trjcat since you didn't tell mdrun a consistent name for
> the
> > files.
> >
> > GROMACS 2016 likely refuses to do your continuation, precisely so that
> you
> > are prompted to say what you actually want, rather than mdrun trying to
> be
> > clever and getting it wrong.
> >
> > Mark
> >
> > On Thu, May 18, 2017 at 11:03 AM Adarsh V. K. <
> adarsh_p13008...@nitc.ac.in>
> > wrote:
> >
> >> Dear gmx users,
> >>
> >> I use Gromacs 5.1.4 for protein ligand simulation. How can I restart a
> >> stopped simulation after a power failure? (used 8 processor cores +
> >> Graphics card GTX 780Ti).
> >>
> >> I have attached the log file along with this mail.
> >>
> >> It appeared that no details appended after restarting simulation (after
> >> power failure at 3.5 ns), Even Though the 'terminal' Ubuntu 16.04 shows
> >> that the simulation successfully restarted from 3.5 ns (used 8 processor
> >> cores + Graphics card GTX 780Ti) and completed the entire 8 ns
> >> simulation...!!. Frames...350 -> 3500 ps (not appended the log file
> after
> >> the restart from 3500ps to 8000ps).
> >>
> >> I used the command (gromacs 5.1.4),
> >>   # gmx mdrun -s md_0_1.tpr -cpi md_0_1_prev.cpt -v
> >>
> >> I also tried, # gmx mdrun -s md_0_1.tpr -cpi md_0_1_prev.cpt -append
> >>
> >> 
> >> 
> >> md_0_1.log : (final)
> >> -
> >> Step   Time Lambda
> >> 1765000 3530.00.0
> >>
> >>Energies (kJ/mol)
> >>G96AngleProper Dih.  Improper Dih.  LJ-14
> >> Coulomb-14
> >> 6.73096e+033.13198e+032.15931e+031.31375e+03
> >> 4.51549e+04
> >> LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
> >> Potential
> >> 3.66659e+05   -7.80170e+03   -2.71529e+064.12416e+03
> >> -2.29382e+06
> >> Kinetic En.   Total EnergyTemperature Pres. DC (bar) Pressure
> >> (bar)
> >> 4.12474e+05   -1.88135e+063.00209e+02   -7.62778e+01
> >> 2.10104e+01
> >>Constr. rmsd
> >> 2.37431e-05
> >> 
> >> -
> >> md.log (final)
> >> --
> >> Step   Time Lambda
> >> 400 8000.00.0
> >>
> >> Writing checkpoint, step 400 at Thu May 18 13:55:01 2017
> >>
> >>
> >>Energies (kJ/mol)
> >>G96AngleProper Dih.  Improper Dih.  LJ-14
> >> Coulomb-14
> >> 6.44959e+033.18212e+032.06343e+031.53953e+03
> >> 4.49878e+04
> >> LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
> >> Potential
> >> 3.66131e+05   -7.78489e+03   -2.71259e+064.78708e+03
> >> -2.29124e+06
> >> Kinetic En.   Total EnergyTemperature Pres. DC (bar) Pressure
> >> (bar)
> >> 4.13852e+05   -1.87738e+063.01212e+02   -7.59495e+01
> >> 5.34060e+01
> >>Constr. rmsd
> >> 2.33151e-05
> >> -
> >> Force evaluation time GPU/CPU: 12.005 ms/12.263 ms = 0.979
> >> For optimal performance this ratio should be close to 1!
> >>
> >>Core t (s)   Wall t (s)(%)
> >>Time:   312346.79739374.380  793.3
> >>  10h56:14
> >>  (ns/day)(hour/ns)
> >> Performance:9.9672.408
> >> Finished mdrun on rank 0 Thu May 18 13:55:02 2017
> >>
> >> 
> >> ---
> >> But while using the command it shows only 3.5 ns of simulation. How to
> >> solve this problem
> >>
> >> 

Re: [gmx-users] (no subject)

[Anshul Lahariya]

hello

plzz use this for query not for hello

On Tue, May 2, 2017 at 4:48 PM, Shivangi Agarwal <
shivangi.agarwal...@gmail.com> wrote:

> Hello
> --
> 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
>
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> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] Gcc

[Anshul Lahariya]

Dear Joao,

U r right, it's my fault, but the thing is that i was tried lot of thing
but not found anything perfect. That's by , i was waiting from weekend for
one answer.

Regards,
Anshul

On Mon, Apr 24, 2017 at 2:53 PM, João Henriques <
joao.m.a.henriq...@gmail.com> wrote:

> Dear Mark and by extension Anshul,
>
> I did make an assumption at the bottom of my previous email, and that was
> uncalled for (despite having good intentions, but that doesn't change
> anything). I apologize for that. That, however, does not overshadow the
> fact that I provided Anshul with all the necessary information in a most
> friendly, voluntary and professional way throughout three separate emails.
>
> Best regards,
> João
>
> On Mon, Apr 24, 2017 at 11:09 AM, Mark Abraham <mark.j.abra...@gmail.com>
> wrote:
>
> > Hi Joao, Anshul and all,
> >
> > Let's all please remember to keep the environment friendly and
> > professional.
> >
> > That means not making assumptions about other people's intentions.
> Learning
> > complex things like simulation science take time, and people often make
> > mistakes when joining new communities, particularly if it's in a language
> > with which they are not fully familiar. :-)
> >
> > That also means remembering that everybody here is volunteering their
> time
> > to help others, and asking only for some of that time when you really
> need
> > it is important if you wish to keep others motivated to help you. Look
> for
> > your own answers first!
> >
> > Please all take a moment to review the thoughts at
> > http://www.gromacs.org/Support/Mailing_Lists (or suggest improvements!)
> >
> > Cheers,
> >
> > Mark
> >
> > On Mon, Apr 24, 2017 at 10:39 AM João Henriques <
> > joao.m.a.henriq...@gmail.com> wrote:
> >
> > > Dear Anshul,
> > >
> > > I thought by movie you meant that you wanted to visually check the
> > > trajectory. ​For PyMOL, google search "pymol movie" produces about
> 31.000
> > > results in 0,31 seconds. The first hit is exactly what you want:
> > >
> > > https://pymolwiki.org/index.php/MovieSchool
> > >
> > > My previous email will still be valid as you'll first need to make
> PyMOL
> > > read your trajectory.
> > >
> > > - - -
> > >
> > > I know you want the exact array of commands you need to input in order
> to
> > > get a movie done, but I will not do that. I believe it is better to
> > provide
> > > the information from which you can learn on your own. It's a bit of the
> > old
> > > "give a man a fish and you feed him for a day; teach a man to fish and
> > you
> > > feed him for a lifetime" proverb. The fact you waited a full weekend
> > > instead of spending a couple of minutes searching and trying yourself
> > tells
> > > me that you're most likely just interested in the "fish", but I'll
> stick
> > to
> > > my belief that learning is better.
> > >
> > > /J
> > >
> > >
> > > On Mon, Apr 24, 2017 at 9:24 AM, Anshul Lahariya <
> > > anshullahariy...@gmail.com
> > > > wrote:
> > >
> > > > hello rahul,
> > > > can u tell me how to make movie??
> > > >
> > > >
> > > > On Fri, Apr 21, 2017 at 3:12 PM, João Henriques <
> > > > joao.m.a.henriq...@gmail.com> wrote:
> > > >
> > > > > ​Plus, installing multiple version of the same software (e.g. gcc)
> is
> > > not
> > > > > problematic at all *when done by someone that knows what he/she is
> > > > doing*.
> > > > > Furthermore, I completely disagree with Vytautas Rakeviius final
> > > advice.
> > > > It
> > > > > wouldn't cross anyone's mind to change OS in order to use a
> different
> > > gcc
> > > > > version. That is ludicrous. I obviously don't recommend that an
> > > > > inexperienced user should start compiling stuff blindly on their
> > > machine,
> > > > > but that is just plain bad practice and impractical.
> > > > >
> > > > > But I digress, this is not really GROMACS related.
> > > > >
> > > > > A nice weekend to everyone!
> > > > > João
> > > > >
> > > > > On Fri, Apr 21, 2017 at 11:21 AM, João Henriques <
> > > > > joao.m.a.henriq...@gmail.com> wrote:
> > > > >
> > &

Re: [gmx-users] Gcc

[Anshul Lahariya]

Dear Joao,

U r right, it's my fault, but the thing is that i was tried lot of thing
but not found anything perfect. That's by , i was waiting from weekend for
one answer.


On Mon, Apr 24, 2017 at 2:53 PM, João Henriques <
joao.m.a.henriq...@gmail.com> wrote:

> Dear Mark and by extension Anshul,
>
> I did make an assumption at the bottom of my previous email, and that was
> uncalled for (despite having good intentions, but that doesn't change
> anything). I apologize for that. That, however, does not overshadow the
> fact that I provided Anshul with all the necessary information in a most
> friendly, voluntary and professional way throughout three separate emails.
>
> Best regards,
> João
>
> On Mon, Apr 24, 2017 at 11:09 AM, Mark Abraham <mark.j.abra...@gmail.com>
> wrote:
>
> > Hi Joao, Anshul and all,
> >
> > Let's all please remember to keep the environment friendly and
> > professional.
> >
> > That means not making assumptions about other people's intentions.
> Learning
> > complex things like simulation science take time, and people often make
> > mistakes when joining new communities, particularly if it's in a language
> > with which they are not fully familiar. :-)
> >
> > That also means remembering that everybody here is volunteering their
> time
> > to help others, and asking only for some of that time when you really
> need
> > it is important if you wish to keep others motivated to help you. Look
> for
> > your own answers first!
> >
> > Please all take a moment to review the thoughts at
> > http://www.gromacs.org/Support/Mailing_Lists (or suggest improvements!)
> >
> > Cheers,
> >
> > Mark
> >
> > On Mon, Apr 24, 2017 at 10:39 AM João Henriques <
> > joao.m.a.henriq...@gmail.com> wrote:
> >
> > > Dear Anshul,
> > >
> > > I thought by movie you meant that you wanted to visually check the
> > > trajectory. ​For PyMOL, google search "pymol movie" produces about
> 31.000
> > > results in 0,31 seconds. The first hit is exactly what you want:
> > >
> > > https://pymolwiki.org/index.php/MovieSchool
> > >
> > > My previous email will still be valid as you'll first need to make
> PyMOL
> > > read your trajectory.
> > >
> > > - - -
> > >
> > > I know you want the exact array of commands you need to input in order
> to
> > > get a movie done, but I will not do that. I believe it is better to
> > provide
> > > the information from which you can learn on your own. It's a bit of the
> > old
> > > "give a man a fish and you feed him for a day; teach a man to fish and
> > you
> > > feed him for a lifetime" proverb. The fact you waited a full weekend
> > > instead of spending a couple of minutes searching and trying yourself
> > tells
> > > me that you're most likely just interested in the "fish", but I'll
> stick
> > to
> > > my belief that learning is better.
> > >
> > > /J
> > >
> > >
> > > On Mon, Apr 24, 2017 at 9:24 AM, Anshul Lahariya <
> > > anshullahariy...@gmail.com
> > > > wrote:
> > >
> > > > hello rahul,
> > > > can u tell me how to make movie??
> > > >
> > > >
> > > > On Fri, Apr 21, 2017 at 3:12 PM, João Henriques <
> > > > joao.m.a.henriq...@gmail.com> wrote:
> > > >
> > > > > ​Plus, installing multiple version of the same software (e.g. gcc)
> is
> > > not
> > > > > problematic at all *when done by someone that knows what he/she is
> > > > doing*.
> > > > > Furthermore, I completely disagree with Vytautas Rakeviius final
> > > advice.
> > > > It
> > > > > wouldn't cross anyone's mind to change OS in order to use a
> different
> > > gcc
> > > > > version. That is ludicrous. I obviously don't recommend that an
> > > > > inexperienced user should start compiling stuff blindly on their
> > > machine,
> > > > > but that is just plain bad practice and impractical.
> > > > >
> > > > > But I digress, this is not really GROMACS related.
> > > > >
> > > > > A nice weekend to everyone!
> > > > > João
> > > > >
> > > > > On Fri, Apr 21, 2017 at 11:21 AM, João Henriques <
> > > > > joao.m.a.henriq...@gmail.com> wrote:
> > > > >
> > > > > &g

Re: [gmx-users] Gcc

[Anshul Lahariya]

hello rahul,
can u tell me how to make movie??


On Fri, Apr 21, 2017 at 3:12 PM, João Henriques <
joao.m.a.henriq...@gmail.com> wrote:

> ​Plus, installing multiple version of the same software (e.g. gcc) is not
> problematic at all *when done by someone that knows what he/she is doing*.
> Furthermore, I completely disagree with Vytautas Rakeviius final advice. It
> wouldn't cross anyone's mind to change OS in order to use a different gcc
> version. That is ludicrous. I obviously don't recommend that an
> inexperienced user should start compiling stuff blindly on their machine,
> but that is just plain bad practice and impractical.
>
> But I digress, this is not really GROMACS related.
>
> A nice weekend to everyone!
> João
>
> On Fri, Apr 21, 2017 at 11:21 AM, João Henriques <
> joao.m.a.henriq...@gmail.com> wrote:
>
> > You have (at the very least) three solutions regarding the movie:
> >
> > [1] Use gmx trjconv (see http://manual.gromacs.org/documentation/5.1.4/
> > onlinehelp/gmx-trjconv.html) to generate a PDB file with the desired
> > trajectory frames. Load and play it in PyMOL et voilà!
> >
> > [2] Install the GROMACS plugin for PyMOL, which will allow you (among
> > other things) to directly read the trajectory files without having to
> > resort to gmx trjconv (see https://pymolwiki.org/index.
> php/GROMACS_Plugin
> > ).
> >
> > [3] Use VMD which can read GROMACS trajectory output files straight out
> of
> > the box (see http://www.ks.uiuc.edu/Research/vmd/).
> >
> > For details regarding gmx trjconv please read the documentation. It is
> > fairly trivial and only you know exactly what system you have at hand.
> Some
> > options will vary depending on that.
> >
> > - - -
> >
> > Regarding gcc, depending on your operating system you can either use a
> > package manager to install the desired version of gcc or compile it
> > yourself. After installing it don't forget to make sure GROMACS knows
> where
> > to search for it, using the -DCMAKE_C_COMPILER=/path/to/gcc flag when
> > running cmake (and probably also -DCMAKE_CXX_COMPILER=/path/to/c++).
> > These paths are obviously fictitious and need to be changed with the
> right
> > ones.
> >
> > Best regards,
> > João
> >
> > On Fri, Apr 21, 2017 at 10:47 AM, Anshul Lahariya <
> > anshullahariy...@gmail.com> wrote:
> >
> >> okkk. it's fine...
> >>
> >>
> >> On Fri, Apr 21, 2017 at 1:06 PM, RAHUL SURESH <drrahulsur...@gmail.com>
> >> wrote:
> >>
> >> > I am out
> >> > Can I say that to u on Monday.) ?
> >> > On Fri, 21 Apr 2017 at 10:28 AM, Anshul Lahariya <
> >> > anshullahariy...@gmail.com>
> >> > wrote:
> >> >
> >> > > yes rahul, i use pymol but dont know how to make movie
> >> > >
> >> > >
> >> > > On Fri, Apr 21, 2017 at 10:09 AM, RAHUL SURESH <
> >> drrahulsur...@gmail.com>
> >> > > wrote:
> >> > >
> >> > > > You must use pymol
> >> > > >
> >> > > >
> >> > > > On Fri, 21 Apr 2017 at 6:35 AM, Anshul Lahariya <
> >> > > > anshullahariy...@gmail.com>
> >> > > > wrote:
> >> > > >
> >> > > > > thanks rahul
> >> > > > >
> >> > > > >
> >> > > > > and how to make md movie for 5ns by command.??
> >> > > > >
> >> > > > >
> >> > > > > On Thu, Apr 20, 2017 at 5:54 PM, RAHUL SURESH <
> >> > drrahulsur...@gmail.com
> >> > > >
> >> > > > > wrote:
> >> > > > >
> >> > > > > > Yum apt-get gcc version
> >> > > > > > Yum update
> >> > > > > > Yum upgrade
> >> > > > > > Yum install
> >> > > > > >
> >> > > > > >
> >> > > > > > On Thu, 20 Apr 2017 at 5:23 PM, Mark Abraham <
> >> > > mark.j.abra...@gmail.com
> >> > > > >
> >> > > > > > wrote:
> >> > > > > >
> >> > > > > > > Hi,
> >> > > > > > >
> >> > > > > > > That's a good question for google or the forums of your
> >> operating
> >> > > > > system,
> >> > > > > > >

Re: [gmx-users] Gcc

[Anshul Lahariya]

okkk. it's fine...


On Fri, Apr 21, 2017 at 1:06 PM, RAHUL SURESH <drrahulsur...@gmail.com>
wrote:

> I am out
> Can I say that to u on Monday.) ?
> On Fri, 21 Apr 2017 at 10:28 AM, Anshul Lahariya <
> anshullahariy...@gmail.com>
> wrote:
>
> > yes rahul, i use pymol but dont know how to make movie
> >
> >
> > On Fri, Apr 21, 2017 at 10:09 AM, RAHUL SURESH <drrahulsur...@gmail.com>
> > wrote:
> >
> > > You must use pymol
> > >
> > >
> > > On Fri, 21 Apr 2017 at 6:35 AM, Anshul Lahariya <
> > > anshullahariy...@gmail.com>
> > > wrote:
> > >
> > > > thanks rahul
> > > >
> > > >
> > > > and how to make md movie for 5ns by command.??
> > > >
> > > >
> > > > On Thu, Apr 20, 2017 at 5:54 PM, RAHUL SURESH <
> drrahulsur...@gmail.com
> > >
> > > > wrote:
> > > >
> > > > > Yum apt-get gcc version
> > > > > Yum update
> > > > > Yum upgrade
> > > > > Yum install
> > > > >
> > > > >
> > > > > On Thu, 20 Apr 2017 at 5:23 PM, Mark Abraham <
> > mark.j.abra...@gmail.com
> > > >
> > > > > wrote:
> > > > >
> > > > > > Hi,
> > > > > >
> > > > > > That's a good question for google or the forums of your operating
> > > > system,
> > > > > > not here. :-)
> > > > > >
> > > > > > Mark
> > > > > >
> > > > > > On Thu, 20 Apr 2017 12:42 Anshul Lahariya <
> > > anshullahariy...@gmail.com>
> > > > > > wrote:
> > > > > >
> > > > > > > hello,
> > > > > > >
> > > > > > > I want to change my gcc and want to install gcc version later
> > than
> > > 5.
> > > > > > > what can i do so i can change the version of gcc to gcc-4.9.4
> > > > > > > --
> > > > > > > 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.
> > > > > >
> > > > > --
> > > > > *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.
> > > > >
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_

Re: [gmx-users] Gcc

[Anshul Lahariya]

yes rahul, i use pymol but dont know how to make movie


On Fri, Apr 21, 2017 at 10:09 AM, RAHUL SURESH <drrahulsur...@gmail.com>
wrote:

> You must use pymol
>
>
> On Fri, 21 Apr 2017 at 6:35 AM, Anshul Lahariya <
> anshullahariy...@gmail.com>
> wrote:
>
> > thanks rahul
> >
> >
> > and how to make md movie for 5ns by command.??
> >
> >
> > On Thu, Apr 20, 2017 at 5:54 PM, RAHUL SURESH <drrahulsur...@gmail.com>
> > wrote:
> >
> > > Yum apt-get gcc version
> > > Yum update
> > > Yum upgrade
> > > Yum install
> > >
> > >
> > > On Thu, 20 Apr 2017 at 5:23 PM, Mark Abraham <mark.j.abra...@gmail.com
> >
> > > wrote:
> > >
> > > > Hi,
> > > >
> > > > That's a good question for google or the forums of your operating
> > system,
> > > > not here. :-)
> > > >
> > > > Mark
> > > >
> > > > On Thu, 20 Apr 2017 12:42 Anshul Lahariya <
> anshullahariy...@gmail.com>
> > > > wrote:
> > > >
> > > > > hello,
> > > > >
> > > > > I want to change my gcc and want to install gcc version later than
> 5.
> > > > > what can i do so i can change the version of gcc to gcc-4.9.4
> > > > > --
> > > > > 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!
> > > >
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> > > >
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> 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!
> > >
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> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
> --
> Gromacs Users mailing list
>
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Re: [gmx-users] Gcc

[Anshul Lahariya]

thanks rahul


and how to make md movie for 5ns by command.??


On Thu, Apr 20, 2017 at 5:54 PM, RAHUL SURESH <drrahulsur...@gmail.com>
wrote:

> Yum apt-get gcc version
> Yum update
> Yum upgrade
> Yum install
>
>
> On Thu, 20 Apr 2017 at 5:23 PM, Mark Abraham <mark.j.abra...@gmail.com>
> wrote:
>
> > Hi,
> >
> > That's a good question for google or the forums of your operating system,
> > not here. :-)
> >
> > Mark
> >
> > On Thu, 20 Apr 2017 12:42 Anshul Lahariya <anshullahariy...@gmail.com>
> > wrote:
> >
> > > hello,
> > >
> > > I want to change my gcc and want to install gcc version later than 5.
> > > what can i do so i can change the version of gcc to gcc-4.9.4
> > > --
> > > 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
> >
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> > 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!
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Re: [gmx-users] make

[Anshul Lahariya]

hello mark,

gcc package is already installed and it is updated.
but cuda want it in later than 5 version. so how can i change the version
of gcc or uninstall that's version


On Thu, Apr 20, 2017 at 5:24 PM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> Like it says, you need to use a version of gcc that suits your version of
> cuda. How to get that done depends what is providing gcc and how your
> operating system provides these packages.
>
> Mark
>
> On Thu, 20 Apr 2017 12:53 Anshul Lahariya <anshullahariy...@gmail.com>
> wrote:
>
> > hello,
> >
> >  i am a new user installing gromacs on my machine.
> >during the installation, i found an error in make command. kindly
> > suggest we correct it.
> >
> >
> > error:-
> > [root@dhcppc99 gromacs-5.1.4-build]# make
> > [  1%] Built target fftwBuild
> > [  1%] Building NVCC (Device) object
> >
> > src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/cuda_
> tools/libgromacs_generated_copyrite_gpu.cu.o
> > nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are
> > deprecated, and may be removed in a future release (Use
> > -Wno-deprecated-gpu-targets to suppress warning).
> > In file included from /usr/local/cuda/include/cuda_runtime.h:78:0,
> >  from :0:
> > /usr/local/cuda/include/host_config.h:119:2: error: #error --
> unsupported
> > GNU version! gcc versions later than 5 are not supported!
> >  #error -- unsupported GNU version! gcc versions later than 5 are not
> > supported!
> >   ^
> > CMake Error at libgromacs_generated_copyrite_gpu.cu.o.Release.cmake:207
> > (message):
> >   Error generating
> >
> >
> > /home/gromacs-5.1.4-build/src/gromacs/CMakeFiles/libgromacs.
> dir/gmxlib/cuda_tools/./libgromacs_generated_copyrite_gpu.cu.o
> >
> >
> > src/gromacs/CMakeFiles/libgromacs.dir/build.make:63: recipe for target
> >
> > 'src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/cuda_
> tools/libgromacs_generated_copyrite_gpu.cu.o'
> > failed
> > make[2]: ***
> >
> > [src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/cuda_
> tools/libgromacs_generated_copyrite_gpu.cu.o]
> > Error 1
> > CMakeFiles/Makefile2:2319: recipe for target
> > 'src/gromacs/CMakeFiles/libgromacs.dir/all' failed
> > make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
> > Makefile:160: recipe for target 'all' failed
> > make: *** [all] Error 2
> > [root@dhcppc99 gromacs-5.1.4-build]#
> > --
> > 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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>
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[gmx-users] make

[Anshul Lahariya]

hello,

 i am a new user installing gromacs on my machine.
   during the installation, i found an error in make command. kindly
suggest we correct it.


error:-
[root@dhcppc99 gromacs-5.1.4-build]# make
[  1%] Built target fftwBuild
[  1%] Building NVCC (Device) object
src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/cuda_tools/libgromacs_generated_copyrite_gpu.cu.o
nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are
deprecated, and may be removed in a future release (Use
-Wno-deprecated-gpu-targets to suppress warning).
In file included from /usr/local/cuda/include/cuda_runtime.h:78:0,
 from :0:
/usr/local/cuda/include/host_config.h:119:2: error: #error -- unsupported
GNU version! gcc versions later than 5 are not supported!
 #error -- unsupported GNU version! gcc versions later than 5 are not
supported!
  ^
CMake Error at libgromacs_generated_copyrite_gpu.cu.o.Release.cmake:207
(message):
  Error generating

/home/gromacs-5.1.4-build/src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/cuda_tools/./libgromacs_generated_copyrite_gpu.cu.o


src/gromacs/CMakeFiles/libgromacs.dir/build.make:63: recipe for target
'src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/cuda_tools/libgromacs_generated_copyrite_gpu.cu.o'
failed
make[2]: ***
[src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/cuda_tools/libgromacs_generated_copyrite_gpu.cu.o]
Error 1
CMakeFiles/Makefile2:2319: recipe for target
'src/gromacs/CMakeFiles/libgromacs.dir/all' failed
make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
Makefile:160: recipe for target 'all' failed
make: *** [all] Error 2
[root@dhcppc99 gromacs-5.1.4-build]#
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[gmx-users] Gcc

[Anshul Lahariya]

hello,

I want to change my gcc and want to install gcc version later than 5.
what can i do so i can change the version of gcc to gcc-4.9.4
-- 
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Re: [gmx-users] extending simulation using GPU, previously ran in CPU

[Anshul Lahariya]

Hi,
   I am a new user and want to enable gpu. hpw to enable gpu?


On Wed, Apr 19, 2017 at 11:11 AM, Mark Abraham 
wrote:

> Hi,
>
> No, but as the log file will report, you will not get per-group energy
> group values in the edr file.
>
> Mark
>
> On Wed, 19 Apr 2017 07:37 Nikhil Maroli  wrote:
>
> > Hello,
> >   extending simulation using GPU which is previously ran using CPU will
> > create any problems in the trajectory ?
> >
> > --
> > Regards,
> > Nikhil Maroli
> > --
> > 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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> >
> > * For (un)subscribe requests visit
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
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>
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Re: [gmx-users] powercut command

[Anshul Lahariya]

i am performing a md of protein ligand complex for 10 ns.
i am using gromacs 5.1.4 on my lappy with 16 gb ram without gpu.

i was performing all the steps without error but found an error in mdrun.

kindly help me to stable my system.
{i am following the protein - ligand complex tutorial of bevan lab}

On Thu, Apr 13, 2017 at 9:11 PM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 4/13/17 11:25 AM, Anshul Lahariya wrote:
>
>> i was failed to diagnose. plzz help me
>>
>>
> Start here:
>
> http://www.catb.org/esr/faqs/smart-questions.html
>
> As I already said, no one on this list can tell anything about your system
> because you have provided no useful diagnostic information or description
> of what you're doing.  If you want free help, you have to make it easy for
> people to help you, with clear, concise communication about what you are
> doing.
>
> -Justin
>
> On Thu, Apr 13, 2017 at 5:30 PM, Justin Lemkul <jalem...@vt.edu> wrote:
>>
>>
>>>
>>> On 4/13/17 7:59 AM, Anshul Lahariya wrote:
>>>
>>> Now i perform a new md, there is a problem with this error
>>>>
>>>>
>>>> [anshu@dhcppc58 AhpE_MSH]$ gmx mdrun -v -deffnm md_1_0
>>>>   :-) GROMACS - gmx mdrun, 2016.2 (-:
>>>>
>>>> GROMACS is written by:
>>>>  Emile Apol  Rossen Apostolov  Herman J.C. BerendsenPar
>>>> Bjelkmar
>>>>  Aldert van Buuren   Rudi van Drunen Anton FeenstraGerrit
>>>> Groenhof
>>>>  Christoph Junghans   Anca HamuraruVincent Hindriksen Dimitrios
>>>> Karkoulis
>>>> Peter KassonJiri Kraus  Carsten Kutzner  Per Larsson
>>>>   Justin A. Lemkul   Magnus Lundborg   Pieter MeulenhoffErik
>>>> Marklund
>>>>Teemu Murtola   Szilard Pall   Sander Pronk  Roland
>>>> Schulz
>>>>   Alexey Shvetsov Michael Shirts Alfons Sijbers Peter
>>>> Tieleman
>>>>   Teemu Virolainen  Christian WennbergMaarten Wolf
>>>>and the project leaders:
>>>> Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
>>>>
>>>> Copyright (c) 1991-2000, University of Groningen, The Netherlands.
>>>> Copyright (c) 2001-2015, The GROMACS development team at
>>>> Uppsala University, Stockholm University and
>>>> the Royal Institute of Technology, Sweden.
>>>> check out http://www.gromacs.org for more information.
>>>>
>>>> GROMACS is free software; you can redistribute it and/or modify it
>>>> under the terms of the GNU Lesser General Public License
>>>> as published by the Free Software Foundation; either version 2.1
>>>> of the License, or (at your option) any later version.
>>>>
>>>> GROMACS:  gmx mdrun, version 2016.2
>>>> Executable:   /usr/bin/gmx
>>>> Data prefix:  /usr
>>>> Working dir:  /home/anshu/Pharma/AhpE_MSH
>>>> Command line:
>>>>   gmx mdrun -v -deffnm md_1_0
>>>>
>>>>
>>>> NOTE: Error occurred during GPU detection:
>>>>   OpenCL error -1001
>>>>   Can not use GPU acceleration, will fall back to CPU kernels.
>>>>
>>>>
>>>> Running on 1 node with total 2 cores, 4 logical cores, 0 compatible GPUs
>>>> Hardware detected:
>>>>   CPU info:
>>>> Vendor: Intel
>>>> Brand:  Intel(R) Core(TM) i7-6500U CPU @ 2.50GHz
>>>> SIMD instructions most likely to fit this hardware: AVX2_256
>>>> SIMD instructions selected at GROMACS compile time: SSE2
>>>>
>>>>   Hardware topology: Full, with devices
>>>>
>>>> Compiled SIMD instructions: SSE2, GROMACS could use AVX2_256 on this
>>>> machine, which is better.
>>>>
>>>> Reading file md_1_0.tpr, VERSION 2016.2 (single precision)
>>>> Changing nstlist from 10 to 25, rlist from 1.4 to 1.431
>>>>
>>>> Using 1 MPI thread
>>>> Using 4 OpenMP threads
>>>>
>>>> starting mdrun 'Protein in water'
>>>> 500 steps,  1.0 ps.
>>>> step 40800, will finish Sun Apr 16 06:11:14 2017
>>>> Step 40875, time 81.75 (ps)  LINCS WARNING
>>>> relative constraint deviation after LINCS:
>>>> rms 0.013405, max 0.537354 (between atoms 1541 and 1542)
>&

Re: [gmx-users] powercut command

[Anshul Lahariya]

i was failed to diagnose. plzz help me

On Thu, Apr 13, 2017 at 5:30 PM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 4/13/17 7:59 AM, Anshul Lahariya wrote:
>
>> Now i perform a new md, there is a problem with this error
>>
>>
>> [anshu@dhcppc58 AhpE_MSH]$ gmx mdrun -v -deffnm md_1_0
>>   :-) GROMACS - gmx mdrun, 2016.2 (-:
>>
>> GROMACS is written by:
>>  Emile Apol  Rossen Apostolov  Herman J.C. BerendsenPar
>> Bjelkmar
>>  Aldert van Buuren   Rudi van Drunen Anton FeenstraGerrit Groenhof
>>  Christoph Junghans   Anca HamuraruVincent Hindriksen Dimitrios
>> Karkoulis
>> Peter KassonJiri Kraus  Carsten Kutzner  Per Larsson
>>   Justin A. Lemkul   Magnus Lundborg   Pieter MeulenhoffErik Marklund
>>Teemu Murtola   Szilard Pall   Sander Pronk  Roland Schulz
>>   Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman
>>   Teemu Virolainen  Christian WennbergMaarten Wolf
>>and the project leaders:
>> Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
>>
>> Copyright (c) 1991-2000, University of Groningen, The Netherlands.
>> Copyright (c) 2001-2015, The GROMACS development team at
>> Uppsala University, Stockholm University and
>> the Royal Institute of Technology, Sweden.
>> check out http://www.gromacs.org for more information.
>>
>> GROMACS is free software; you can redistribute it and/or modify it
>> under the terms of the GNU Lesser General Public License
>> as published by the Free Software Foundation; either version 2.1
>> of the License, or (at your option) any later version.
>>
>> GROMACS:  gmx mdrun, version 2016.2
>> Executable:   /usr/bin/gmx
>> Data prefix:  /usr
>> Working dir:  /home/anshu/Pharma/AhpE_MSH
>> Command line:
>>   gmx mdrun -v -deffnm md_1_0
>>
>>
>> NOTE: Error occurred during GPU detection:
>>   OpenCL error -1001
>>   Can not use GPU acceleration, will fall back to CPU kernels.
>>
>>
>> Running on 1 node with total 2 cores, 4 logical cores, 0 compatible GPUs
>> Hardware detected:
>>   CPU info:
>> Vendor: Intel
>> Brand:  Intel(R) Core(TM) i7-6500U CPU @ 2.50GHz
>> SIMD instructions most likely to fit this hardware: AVX2_256
>> SIMD instructions selected at GROMACS compile time: SSE2
>>
>>   Hardware topology: Full, with devices
>>
>> Compiled SIMD instructions: SSE2, GROMACS could use AVX2_256 on this
>> machine, which is better.
>>
>> Reading file md_1_0.tpr, VERSION 2016.2 (single precision)
>> Changing nstlist from 10 to 25, rlist from 1.4 to 1.431
>>
>> Using 1 MPI thread
>> Using 4 OpenMP threads
>>
>> starting mdrun 'Protein in water'
>> 500 steps,  1.0 ps.
>> step 40800, will finish Sun Apr 16 06:11:14 2017
>> Step 40875, time 81.75 (ps)  LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.013405, max 0.537354 (between atoms 1541 and 1542)
>> bonds that rotated more than 30 degrees:
>>  atom 1 atom 2  angle  previous, current, constraint length
>>1541   1542   90.00.1330   0.2045  0.1330
>>
>> step 40875: One or more water molecules can not be settled.
>> Check for bad contacts and/or reduce the timestep if appropriate.
>> Wrote pdb files with previous and current coordinates
>> Segmentation fault (core dumped)
>> [anshu@dhcppc58 AhpE_MSH]$
>>
>>
>>
> Your system is unstable.  Follow the link I posted before.  It's
> impossible for anyone to diagnose anything based on this generic failure
> message.
>
> -Justin
>
>
>>
>>
>>
>> On Thu, Apr 13, 2017 at 4:45 PM, Anshul Lahariya <
>> anshullahariy...@gmail.com
>>
>>> wrote:
>>>
>>
>> okkk,,, thank u justin sir
>>>
>>> On Thu, Apr 13, 2017 at 3:51 PM, Justin Lemkul <jalem...@vt.edu> wrote:
>>>
>>>
>>>>
>>>> On 4/13/17 6:19 AM, Anshul Lahariya wrote:
>>>>
>>>> now i got this error
>>>>>
>>>>>
>>>>> Program: gmx mdrun, version 2016.2
>>>>> Source file: src/gromacs/mdlib/constr.cpp (line 167)
>>>>>
>>>>> Fatal error:
>>>>> Too many LINCS warnings (1000)
>>>>> If you know what you are doing you can adjust the lincs warning
>>>>> threshold in
>>>>> your mdp file

Re: [gmx-users] powercut command

[Anshul Lahariya]

Now i perform a new md, there is a problem with this error


[anshu@dhcppc58 AhpE_MSH]$ gmx mdrun -v -deffnm md_1_0
  :-) GROMACS - gmx mdrun, 2016.2 (-:

GROMACS is written by:
 Emile Apol  Rossen Apostolov  Herman J.C. BerendsenPar
Bjelkmar
 Aldert van Buuren   Rudi van Drunen Anton FeenstraGerrit Groenhof
 Christoph Junghans   Anca HamuraruVincent Hindriksen Dimitrios
Karkoulis
Peter KassonJiri Kraus  Carsten Kutzner  Per Larsson
  Justin A. Lemkul   Magnus Lundborg   Pieter MeulenhoffErik Marklund
   Teemu Murtola   Szilard Pall   Sander Pronk  Roland Schulz
  Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman
  Teemu Virolainen  Christian WennbergMaarten Wolf
   and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2015, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:  gmx mdrun, version 2016.2
Executable:   /usr/bin/gmx
Data prefix:  /usr
Working dir:  /home/anshu/Pharma/AhpE_MSH
Command line:
  gmx mdrun -v -deffnm md_1_0


NOTE: Error occurred during GPU detection:
  OpenCL error -1001
  Can not use GPU acceleration, will fall back to CPU kernels.


Running on 1 node with total 2 cores, 4 logical cores, 0 compatible GPUs
Hardware detected:
  CPU info:
Vendor: Intel
Brand:  Intel(R) Core(TM) i7-6500U CPU @ 2.50GHz
SIMD instructions most likely to fit this hardware: AVX2_256
SIMD instructions selected at GROMACS compile time: SSE2

  Hardware topology: Full, with devices

Compiled SIMD instructions: SSE2, GROMACS could use AVX2_256 on this
machine, which is better.

Reading file md_1_0.tpr, VERSION 2016.2 (single precision)
Changing nstlist from 10 to 25, rlist from 1.4 to 1.431

Using 1 MPI thread
Using 4 OpenMP threads

starting mdrun 'Protein in water'
500 steps,  1.0 ps.
step 40800, will finish Sun Apr 16 06:11:14 2017
Step 40875, time 81.75 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.013405, max 0.537354 (between atoms 1541 and 1542)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   1541   1542   90.00.1330   0.2045  0.1330

step 40875: One or more water molecules can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Segmentation fault (core dumped)
[anshu@dhcppc58 AhpE_MSH]$






On Thu, Apr 13, 2017 at 4:45 PM, Anshul Lahariya <anshullahariy...@gmail.com
> wrote:

> okkk,,, thank u justin sir
>
> On Thu, Apr 13, 2017 at 3:51 PM, Justin Lemkul <jalem...@vt.edu> wrote:
>
>>
>>
>> On 4/13/17 6:19 AM, Anshul Lahariya wrote:
>>
>>> now i got this error
>>>
>>>
>>> Program: gmx mdrun, version 2016.2
>>> Source file: src/gromacs/mdlib/constr.cpp (line 167)
>>>
>>> Fatal error:
>>> Too many LINCS warnings (1000)
>>> If you know what you are doing you can adjust the lincs warning
>>> threshold in
>>> your mdp file
>>> or set the environment variable GMX_MAXCONSTRWARN to -1,
>>> but normally it is better to fix the problem
>>>
>>> For more information and tips for troubleshooting, please check the
>>> GROMACS
>>> website at http://www.gromacs.org/Documentation/Errors
>>> ---
>>> [root@dhcppc58 AhpE_MSH]#
>>>
>>>
>> You simulation is crashing and cannot be continued.  Consult
>> http://www.gromacs.org/Documentation/Terminology/Blowing_Up#
>> Diagnosing_an_Unstable_System
>>
>> Also, do NOT do your normal work as root.  That is extremely dangerous.
>>
>> -Justin
>>
>>
>>
>>> On Thu, Apr 13, 2017 at 3:43 PM, Anshul Lahariya <
>>> anshullahariy...@gmail.com
>>>
>>>> wrote:
>>>>
>>>
>>> thankss tasneem.
>>>>
>>>> let me try.
>>>>
>>>>
>>>> On Thu, Apr 13, 2017 at 3:40 PM, Anshul Lahariya <
>>>> anshullahariy...@gmail.com> wrote:
>>>>
>>>> powercut take place and md stops, so i want to continue my md
>>>>>
>>

Re: [gmx-users] powercut command

[Anshul Lahariya]

okkk,,, thank u justin sir

On Thu, Apr 13, 2017 at 3:51 PM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 4/13/17 6:19 AM, Anshul Lahariya wrote:
>
>> now i got this error
>>
>>
>> Program: gmx mdrun, version 2016.2
>> Source file: src/gromacs/mdlib/constr.cpp (line 167)
>>
>> Fatal error:
>> Too many LINCS warnings (1000)
>> If you know what you are doing you can adjust the lincs warning threshold
>> in
>> your mdp file
>> or set the environment variable GMX_MAXCONSTRWARN to -1,
>> but normally it is better to fix the problem
>>
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>> ---
>> [root@dhcppc58 AhpE_MSH]#
>>
>>
> You simulation is crashing and cannot be continued.  Consult
> http://www.gromacs.org/Documentation/Terminology/Blowing_Up#
> Diagnosing_an_Unstable_System
>
> Also, do NOT do your normal work as root.  That is extremely dangerous.
>
> -Justin
>
>
>
>> On Thu, Apr 13, 2017 at 3:43 PM, Anshul Lahariya <
>> anshullahariy...@gmail.com
>>
>>> wrote:
>>>
>>
>> thankss tasneem.
>>>
>>> let me try.
>>>
>>>
>>> On Thu, Apr 13, 2017 at 3:40 PM, Anshul Lahariya <
>>> anshullahariy...@gmail.com> wrote:
>>>
>>> powercut take place and md stops, so i want to continue my md
>>>>
>>>>
>>>>
>>>>
>>>> [root@dhcppc58 AhpE_MSH]# gmx mdrun -v -s md_1_0.tpr -e md_1_0.edr -g
>>>> md_1_0.log -o md_1_0.xtc -cpi md_1_0.cpt -cpo md_1_0.cpt -append
>>>>   :-) GROMACS - gmx mdrun, 2016.2 (-:
>>>>
>>>> GROMACS is written by:
>>>>  Emile Apol  Rossen Apostolov  Herman J.C. BerendsenPar
>>>> Bjelkmar
>>>>  Aldert van Buuren   Rudi van Drunen Anton FeenstraGerrit
>>>> Groenhof
>>>>  Christoph Junghans   Anca HamuraruVincent Hindriksen Dimitrios
>>>> Karkoulis
>>>> Peter KassonJiri Kraus  Carsten Kutzner  Per
>>>> Larsson
>>>>   Justin A. Lemkul   Magnus Lundborg   Pieter MeulenhoffErik
>>>> Marklund
>>>>Teemu Murtola   Szilard Pall   Sander Pronk  Roland
>>>> Schulz
>>>>   Alexey Shvetsov Michael Shirts Alfons Sijbers Peter
>>>> Tieleman
>>>>   Teemu Virolainen  Christian WennbergMaarten Wolf
>>>>and the project leaders:
>>>> Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
>>>>
>>>> Copyright (c) 1991-2000, University of Groningen, The Netherlands.
>>>> Copyright (c) 2001-2015, The GROMACS development team at
>>>> Uppsala University, Stockholm University and
>>>> the Royal Institute of Technology, Sweden.
>>>> check out http://www.gromacs.org for more information.
>>>>
>>>> GROMACS is free software; you can redistribute it and/or modify it
>>>> under the terms of the GNU Lesser General Public License
>>>> as published by the Free Software Foundation; either version 2.1
>>>> of the License, or (at your option) any later version.
>>>>
>>>> GROMACS:  gmx mdrun, version 2016.2
>>>> Executable:   /usr/bin/gmx
>>>> Data prefix:  /usr
>>>> Working dir:  /home/anshu/Pharma/AhpE_MSH
>>>> Command line:
>>>>   gmx mdrun -v -s md_1_0.tpr -e md_1_0.edr -g md_1_0.log -o md_1_0.xtc
>>>> -cpi md_1_0.cpt -cpo md_1_0.cpt -append
>>>>
>>>>
>>>> ---
>>>> Program: gmx mdrun, version 2016.2
>>>> Source file: src/gromacs/commandline/cmdlineparser.cpp (line 235)
>>>> Function:void gmx::CommandLineParser::parse(int*, char**)
>>>>
>>>> Error in user input:
>>>> Invalid command-line options
>>>>   In command-line option -o
>>>> File name 'md_1_0.xtc' cannot be used for this option.
>>>> Only the following extensions are possible:
>>>>   .trr, .cpt, .tng
>>>>
>>>> For more information and tips for troubleshooting, please check the
>>>> GROMACS
>>>> website at http://www.gromacs.org/Documentation/Errors
>>>&

Re: [gmx-users] powercut command

[Anshul Lahariya]

now i got this error


Program: gmx mdrun, version 2016.2
Source file: src/gromacs/mdlib/constr.cpp (line 167)

Fatal error:
Too many LINCS warnings (1000)
If you know what you are doing you can adjust the lincs warning threshold in
your mdp file
or set the environment variable GMX_MAXCONSTRWARN to -1,
but normally it is better to fix the problem

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---
[root@dhcppc58 AhpE_MSH]#


On Thu, Apr 13, 2017 at 3:43 PM, Anshul Lahariya <anshullahariy...@gmail.com
> wrote:

> thankss tasneem.
>
> let me try.
>
>
> On Thu, Apr 13, 2017 at 3:40 PM, Anshul Lahariya <
> anshullahariy...@gmail.com> wrote:
>
>> powercut take place and md stops, so i want to continue my md
>>
>>
>>
>>
>> [root@dhcppc58 AhpE_MSH]# gmx mdrun -v -s md_1_0.tpr -e md_1_0.edr -g
>> md_1_0.log -o md_1_0.xtc -cpi md_1_0.cpt -cpo md_1_0.cpt -append
>>   :-) GROMACS - gmx mdrun, 2016.2 (-:
>>
>> GROMACS is written by:
>>  Emile Apol  Rossen Apostolov  Herman J.C. BerendsenPar
>> Bjelkmar
>>  Aldert van Buuren   Rudi van Drunen Anton FeenstraGerrit
>> Groenhof
>>  Christoph Junghans   Anca HamuraruVincent Hindriksen Dimitrios
>> Karkoulis
>> Peter KassonJiri Kraus  Carsten Kutzner  Per
>> Larsson
>>   Justin A. Lemkul   Magnus Lundborg   Pieter MeulenhoffErik
>> Marklund
>>Teemu Murtola   Szilard Pall   Sander Pronk  Roland
>> Schulz
>>   Alexey Shvetsov Michael Shirts Alfons Sijbers Peter
>> Tieleman
>>   Teemu Virolainen  Christian WennbergMaarten Wolf
>>and the project leaders:
>> Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
>>
>> Copyright (c) 1991-2000, University of Groningen, The Netherlands.
>> Copyright (c) 2001-2015, The GROMACS development team at
>> Uppsala University, Stockholm University and
>> the Royal Institute of Technology, Sweden.
>> check out http://www.gromacs.org for more information.
>>
>> GROMACS is free software; you can redistribute it and/or modify it
>> under the terms of the GNU Lesser General Public License
>> as published by the Free Software Foundation; either version 2.1
>> of the License, or (at your option) any later version.
>>
>> GROMACS:  gmx mdrun, version 2016.2
>> Executable:   /usr/bin/gmx
>> Data prefix:  /usr
>> Working dir:  /home/anshu/Pharma/AhpE_MSH
>> Command line:
>>   gmx mdrun -v -s md_1_0.tpr -e md_1_0.edr -g md_1_0.log -o md_1_0.xtc
>> -cpi md_1_0.cpt -cpo md_1_0.cpt -append
>>
>>
>> ---
>> Program: gmx mdrun, version 2016.2
>> Source file: src/gromacs/commandline/cmdlineparser.cpp (line 235)
>> Function:void gmx::CommandLineParser::parse(int*, char**)
>>
>> Error in user input:
>> Invalid command-line options
>>   In command-line option -o
>> File name 'md_1_0.xtc' cannot be used for this option.
>> Only the following extensions are possible:
>>   .trr, .cpt, .tng
>>
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>> ---
>> [root@dhcppc58 AhpE_MSH]# ^C
>> [root@dhcppc58 AhpE_MSH]#
>>
>>
>>
>>
>> plzzz help me and suggest me the command for continuation of my md run
>>
>> On Thu, Apr 13, 2017 at 3:34 PM, Tasneem Kausar <
>> tasneemkausa...@gmail.com> wrote:
>>
>>> please give the exact command and error message.
>>>
>>> On Thu, Apr 13, 2017 at 3:30 PM, Anshul Lahariya <
>>> anshullahariy...@gmail.com
>>> > wrote:
>>>
>>> > dear das sir,
>>> >
>>> > -cpi was already added to the command but my problem is not solved
>>> >
>>> > On Thu, Apr 13, 2017 at 3:24 PM, Anshul Lahariya <
>>> > anshullahariy...@gmail.com
>>> > > wrote:
>>> >
>>> > > error says, xtc file is not used for this option . plzz use trr,
>>> cpt, tng
>>> > >
>>> > >
>>> > > help me out
>>> > >
>>> > > On Thu, Apr 13, 2017 at 11:29 AM, Amir Zeb <zebami...@gmail.com>
>>> wrote:
>&

Re: [gmx-users] powercut command

[Anshul Lahariya]

thankss tasneem.

let me try.


On Thu, Apr 13, 2017 at 3:40 PM, Anshul Lahariya <anshullahariy...@gmail.com
> wrote:

> powercut take place and md stops, so i want to continue my md
>
>
>
>
> [root@dhcppc58 AhpE_MSH]# gmx mdrun -v -s md_1_0.tpr -e md_1_0.edr -g
> md_1_0.log -o md_1_0.xtc -cpi md_1_0.cpt -cpo md_1_0.cpt -append
>   :-) GROMACS - gmx mdrun, 2016.2 (-:
>
> GROMACS is written by:
>  Emile Apol  Rossen Apostolov  Herman J.C. BerendsenPar
> Bjelkmar
>  Aldert van Buuren   Rudi van Drunen Anton FeenstraGerrit
> Groenhof
>  Christoph Junghans   Anca HamuraruVincent Hindriksen Dimitrios
> Karkoulis
> Peter KassonJiri Kraus  Carsten Kutzner  Per
> Larsson
>   Justin A. Lemkul   Magnus Lundborg   Pieter MeulenhoffErik
> Marklund
>Teemu Murtola   Szilard Pall   Sander Pronk  Roland
> Schulz
>   Alexey Shvetsov Michael Shirts Alfons Sijbers Peter
> Tieleman
>   Teemu Virolainen  Christian WennbergMaarten Wolf
>and the project leaders:
> Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
>
> Copyright (c) 1991-2000, University of Groningen, The Netherlands.
> Copyright (c) 2001-2015, The GROMACS development team at
> Uppsala University, Stockholm University and
> the Royal Institute of Technology, Sweden.
> check out http://www.gromacs.org for more information.
>
> GROMACS is free software; you can redistribute it and/or modify it
> under the terms of the GNU Lesser General Public License
> as published by the Free Software Foundation; either version 2.1
> of the License, or (at your option) any later version.
>
> GROMACS:  gmx mdrun, version 2016.2
> Executable:   /usr/bin/gmx
> Data prefix:  /usr
> Working dir:  /home/anshu/Pharma/AhpE_MSH
> Command line:
>   gmx mdrun -v -s md_1_0.tpr -e md_1_0.edr -g md_1_0.log -o md_1_0.xtc
> -cpi md_1_0.cpt -cpo md_1_0.cpt -append
>
>
> ---
> Program: gmx mdrun, version 2016.2
> Source file: src/gromacs/commandline/cmdlineparser.cpp (line 235)
> Function:void gmx::CommandLineParser::parse(int*, char**)
>
> Error in user input:
> Invalid command-line options
>   In command-line option -o
> File name 'md_1_0.xtc' cannot be used for this option.
> Only the following extensions are possible:
>   .trr, .cpt, .tng
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
> [root@dhcppc58 AhpE_MSH]# ^C
> [root@dhcppc58 AhpE_MSH]#
>
>
>
>
> plzzz help me and suggest me the command for continuation of my md run
>
> On Thu, Apr 13, 2017 at 3:34 PM, Tasneem Kausar <tasneemkausa...@gmail.com
> > wrote:
>
>> please give the exact command and error message.
>>
>> On Thu, Apr 13, 2017 at 3:30 PM, Anshul Lahariya <
>> anshullahariy...@gmail.com
>> > wrote:
>>
>> > dear das sir,
>> >
>> > -cpi was already added to the command but my problem is not solved
>> >
>> > On Thu, Apr 13, 2017 at 3:24 PM, Anshul Lahariya <
>> > anshullahariy...@gmail.com
>> > > wrote:
>> >
>> > > error says, xtc file is not used for this option . plzz use trr, cpt,
>> tng
>> > >
>> > >
>> > > help me out
>> > >
>> > > On Thu, Apr 13, 2017 at 11:29 AM, Amir Zeb <zebami...@gmail.com>
>> wrote:
>> > >
>> > >> please put this command line
>> > >> gmx mdrun -v -s xxx.tpr -c xxx.gro -g xxx.log -e xxx.edr -cpi
>> xxx.cpt -o
>> > >> md_1_0.xtc
>> > >>
>> > >> good luck
>> > >>
>> > >> On Wed, Apr 12, 2017 at 10:42 PM, Anshul Lahariya <
>> > >> anshullahariy...@gmail.com> wrote:
>> > >>
>> > >> > My md was running. Suddenly power supply was cuts due to some
>> reason
>> > >> and my
>> > >> > my MD stops..
>> > >> > To continue my MD, I use command:-
>> > >> >
>> > >> >
>> > >> > gmx mdrun -v -s 10ns.tpr -e 10ns.edr -g 10ns.log -10ns.xtc -cpi
>> > 10ns.cpt
>> > >> > -cpo 10ns.cpt -append
>> > >> >
>> > >> >
>> > >> >
>> > >> > but shows error.
>> > >> >
>> > >> >
>> > &

Re: [gmx-users] powercut command

[Anshul Lahariya]

powercut take place and md stops, so i want to continue my md




[root@dhcppc58 AhpE_MSH]# gmx mdrun -v -s md_1_0.tpr -e md_1_0.edr -g
md_1_0.log -o md_1_0.xtc -cpi md_1_0.cpt -cpo md_1_0.cpt -append
  :-) GROMACS - gmx mdrun, 2016.2 (-:

GROMACS is written by:
 Emile Apol  Rossen Apostolov  Herman J.C. BerendsenPar
Bjelkmar
 Aldert van Buuren   Rudi van Drunen Anton FeenstraGerrit Groenhof
 Christoph Junghans   Anca HamuraruVincent Hindriksen Dimitrios
Karkoulis
Peter KassonJiri Kraus  Carsten Kutzner  Per Larsson
  Justin A. Lemkul   Magnus Lundborg   Pieter MeulenhoffErik Marklund
   Teemu Murtola   Szilard Pall   Sander Pronk  Roland Schulz
  Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman
  Teemu Virolainen  Christian WennbergMaarten Wolf
   and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2015, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:  gmx mdrun, version 2016.2
Executable:   /usr/bin/gmx
Data prefix:  /usr
Working dir:  /home/anshu/Pharma/AhpE_MSH
Command line:
  gmx mdrun -v -s md_1_0.tpr -e md_1_0.edr -g md_1_0.log -o md_1_0.xtc -cpi
md_1_0.cpt -cpo md_1_0.cpt -append


---
Program: gmx mdrun, version 2016.2
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 235)
Function:void gmx::CommandLineParser::parse(int*, char**)

Error in user input:
Invalid command-line options
  In command-line option -o
File name 'md_1_0.xtc' cannot be used for this option.
Only the following extensions are possible:
  .trr, .cpt, .tng

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---
[root@dhcppc58 AhpE_MSH]# ^C
[root@dhcppc58 AhpE_MSH]#




plzzz help me and suggest me the command for continuation of my md run

On Thu, Apr 13, 2017 at 3:34 PM, Tasneem Kausar <tasneemkausa...@gmail.com>
wrote:

> please give the exact command and error message.
>
> On Thu, Apr 13, 2017 at 3:30 PM, Anshul Lahariya <
> anshullahariy...@gmail.com
> > wrote:
>
> > dear das sir,
> >
> > -cpi was already added to the command but my problem is not solved
> >
> > On Thu, Apr 13, 2017 at 3:24 PM, Anshul Lahariya <
> > anshullahariy...@gmail.com
> > > wrote:
> >
> > > error says, xtc file is not used for this option . plzz use trr, cpt,
> tng
> > >
> > >
> > > help me out
> > >
> > > On Thu, Apr 13, 2017 at 11:29 AM, Amir Zeb <zebami...@gmail.com>
> wrote:
> > >
> > >> please put this command line
> > >> gmx mdrun -v -s xxx.tpr -c xxx.gro -g xxx.log -e xxx.edr -cpi xxx.cpt
> -o
> > >> md_1_0.xtc
> > >>
> > >> good luck
> > >>
> > >> On Wed, Apr 12, 2017 at 10:42 PM, Anshul Lahariya <
> > >> anshullahariy...@gmail.com> wrote:
> > >>
> > >> > My md was running. Suddenly power supply was cuts due to some reason
> > >> and my
> > >> > my MD stops..
> > >> > To continue my MD, I use command:-
> > >> >
> > >> >
> > >> > gmx mdrun -v -s 10ns.tpr -e 10ns.edr -g 10ns.log -10ns.xtc -cpi
> > 10ns.cpt
> > >> > -cpo 10ns.cpt -append
> > >> >
> > >> >
> > >> >
> > >> > but shows error.
> > >> >
> > >> >
> > >> > Error in user input:
> > >> > Invalid command-line options
> > >> > Unknown command-line option -md_1_0.xtc
> > >> >
> > >> > For more information and tips for troubleshooting, please check the
> > >> GROMACS
> > >> > website at http://www.gromacs.org/Documentation/Errors
> > >> > ---
> > >> > [root@dhcppc58 AhpE_MSH]#
> > >> >
> > >> >
> > >> >
> > >> > Plzz.. help me out
> > >> > --
> > >> > Groma

Re: [gmx-users] powercut command

[Anshul Lahariya]

dear das sir,

-cpi was already added to the command but my problem is not solved

On Thu, Apr 13, 2017 at 3:24 PM, Anshul Lahariya <anshullahariy...@gmail.com
> wrote:

> error says, xtc file is not used for this option . plzz use trr, cpt, tng
>
>
> help me out
>
> On Thu, Apr 13, 2017 at 11:29 AM, Amir Zeb <zebami...@gmail.com> wrote:
>
>> please put this command line
>> gmx mdrun -v -s xxx.tpr -c xxx.gro -g xxx.log -e xxx.edr -cpi xxx.cpt -o
>> md_1_0.xtc
>>
>> good luck
>>
>> On Wed, Apr 12, 2017 at 10:42 PM, Anshul Lahariya <
>> anshullahariy...@gmail.com> wrote:
>>
>> > My md was running. Suddenly power supply was cuts due to some reason
>> and my
>> > my MD stops..
>> > To continue my MD, I use command:-
>> >
>> >
>> > gmx mdrun -v -s 10ns.tpr -e 10ns.edr -g 10ns.log -10ns.xtc -cpi 10ns.cpt
>> > -cpo 10ns.cpt -append
>> >
>> >
>> >
>> > but shows error.
>> >
>> >
>> > Error in user input:
>> > Invalid command-line options
>> > Unknown command-line option -md_1_0.xtc
>> >
>> > For more information and tips for troubleshooting, please check the
>> GROMACS
>> > website at http://www.gromacs.org/Documentation/Errors
>> > ---
>> > [root@dhcppc58 AhpE_MSH]#
>> >
>> >
>> >
>> > Plzz.. help me out
>> > --
>> > 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!
>>
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>>
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>>
>
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Re: [gmx-users] powercut command

[Anshul Lahariya]

error says, xtc file is not used for this option . plzz use trr, cpt, tng


help me out

On Thu, Apr 13, 2017 at 11:29 AM, Amir Zeb <zebami...@gmail.com> wrote:

> please put this command line
> gmx mdrun -v -s xxx.tpr -c xxx.gro -g xxx.log -e xxx.edr -cpi xxx.cpt -o
> md_1_0.xtc
>
> good luck
>
> On Wed, Apr 12, 2017 at 10:42 PM, Anshul Lahariya <
> anshullahariy...@gmail.com> wrote:
>
> > My md was running. Suddenly power supply was cuts due to some reason and
> my
> > my MD stops..
> > To continue my MD, I use command:-
> >
> >
> > gmx mdrun -v -s 10ns.tpr -e 10ns.edr -g 10ns.log -10ns.xtc -cpi 10ns.cpt
> > -cpo 10ns.cpt -append
> >
> >
> >
> > but shows error.
> >
> >
> > Error in user input:
> > Invalid command-line options
> > Unknown command-line option -md_1_0.xtc
> >
> > For more information and tips for troubleshooting, please check the
> GROMACS
> > website at http://www.gromacs.org/Documentation/Errors
> > ---
> > [root@dhcppc58 AhpE_MSH]#
> >
> >
> >
> > Plzz.. help me out
> > --
> > 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!
>
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>
> * For (un)subscribe requests visit
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> send a mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] powercut command

[Anshul Lahariya]

This is a error that i got during mdrun. plzzz help..



Program: gmx mdrun, version 2016.2
Source file: src/gromacs/mdlib/constr.cpp (line 167)

Fatal error:
Too many LINCS warnings (1000)
If you know what you are doing you can adjust the lincs warning threshold in
your mdp file
or set the environment variable GMX_MAXCONSTRWARN to -1,
but normally it is better to fix the problem

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---
[root@dhcppc58 AhpE_MSH]# Program: gmx mdrun, version 2016.2


On Thu, Apr 13, 2017 at 12:06 PM, Anshul Lahariya <
anshullahariy...@gmail.com> wrote:

> Thank u so much
>
> #Devashish Das
>
>
> On Thu, Apr 13, 2017 at 11:30 AM, Devashish_Das <dasdevashish...@gmail.com
> > wrote:
>
>> Please use to resume:
>>
>> gmx mdrun -v -deffnm 10ns -cpi 10ns.cpt
>>
>>
>>
>>
>> On Thu, Apr 13, 2017 at 11:12 AM, Anshul Lahariya <
>> anshullahariy...@gmail.com> wrote:
>>
>> > My md was running. Suddenly power supply was cuts due to some reason
>> and my
>> > my MD stops..
>> > To continue my MD, I use command:-
>> >
>> >
>> > gmx mdrun -v -s 10ns.tpr -e 10ns.edr -g 10ns.log -10ns.xtc -cpi 10ns.cpt
>> > -cpo 10ns.cpt -append
>> >
>> >
>> >
>> > but shows error.
>> >
>> >
>> > Error in user input:
>> > Invalid command-line options
>> > Unknown command-line option -md_1_0.xtc
>> >
>> > For more information and tips for troubleshooting, please check the
>> GROMACS
>> > website at http://www.gromacs.org/Documentation/Errors
>> > ---
>> > [root@dhcppc58 AhpE_MSH]#
>> >
>> >
>> >
>> > Plzz.. help me out
>> > --
>> > 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,
>>
>> Devashish Das
>> --
>> 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.
>>
>
>
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Re: [gmx-users] powercut command

[Anshul Lahariya]

Thank u so much

#Devashish Das


On Thu, Apr 13, 2017 at 11:30 AM, Devashish_Das <dasdevashish...@gmail.com>
wrote:

> Please use to resume:
>
> gmx mdrun -v -deffnm 10ns -cpi 10ns.cpt
>
>
>
>
> On Thu, Apr 13, 2017 at 11:12 AM, Anshul Lahariya <
> anshullahariy...@gmail.com> wrote:
>
> > My md was running. Suddenly power supply was cuts due to some reason and
> my
> > my MD stops..
> > To continue my MD, I use command:-
> >
> >
> > gmx mdrun -v -s 10ns.tpr -e 10ns.edr -g 10ns.log -10ns.xtc -cpi 10ns.cpt
> > -cpo 10ns.cpt -append
> >
> >
> >
> > but shows error.
> >
> >
> > Error in user input:
> > Invalid command-line options
> > Unknown command-line option -md_1_0.xtc
> >
> > For more information and tips for troubleshooting, please check the
> GROMACS
> > website at http://www.gromacs.org/Documentation/Errors
> > ---
> > [root@dhcppc58 AhpE_MSH]#
> >
> >
> >
> > Plzz.. help me out
> > --
> > 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,
>
> Devashish Das
> --
> 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] powercut command

[Anshul Lahariya]

My md was running. Suddenly power supply was cuts due to some reason and my
my MD stops..
To continue my MD, I use command:-


gmx mdrun -v -s 10ns.tpr -e 10ns.edr -g 10ns.log -10ns.xtc -cpi 10ns.cpt
-cpo 10ns.cpt -append



but shows error.


Error in user input:
Invalid command-line options
Unknown command-line option -md_1_0.xtc

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---
[root@dhcppc58 AhpE_MSH]#



Plzz.. help me out
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