date:20170320

[gmx-users] Regarding extending simulations

2017-03-20 Thread Dilip H N

Hello,
I ran a md run of 20ns [1000*.002] and i got the files as md.edr,
md.log, md.tpr, md.gro, md.xtc, md.cpt etc.,
Now i want to extend/continue my simulation from 20 ns to again 20 ns
(total 40 ns).
So i gave the command as -
gmx convert-tpr -s md.tpr - extend 2 -o md1.tpr
gmx mdrun -v -s md1.tpr -cpi md.cpt -append

But i am getting the following errors..

Output file appending has been requested,
but some output files listed in the checkpoint file md.cpt
are not present or not named as the output files by the current program:
Expect output files present:
  md.log

Expected output files not present or named differently:
  md.xtc
  md.trr
  md.edr

---
Program: gmx mdrun, version 2016.2
Source file: src/gromacs/mdrunutility/handlerestart.cpp (line 177)

Fatal error:
File appending requested, but 3 of the 4 output files are not present or are
named differently. For safety reasons, GROMACS-2016 and later only allows
file
appending to be used when all files have the same names as they had in the
original run. Checkpointing is merely intended for plain continuation of
runs.
For safety reasons you must specify all file names (e.g. with -deffnm), and
all these files must match the names used in the run prior to checkpointing
since we will append to them by default. If the files are not available, you
can add the -noappend flag to mdrun and write separate new parts. For mere
concatenation of files, you should use the gmx trjcat tool instead.

why is this error coming in spite i have all the above files in my workin
directory and i have not changed any names neither have edited any of
those

-- 
With Best Regards,

DILIP.H.N
Research Scholar,
Department of Chemistry, NITK.



   Sent with Mailtrack

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Re: [gmx-users] mdp options for REMD

2017-03-20 Thread YanhuaOuyang

Dear Mark,
Do you mean that both  "generate at 300K but themostat at 
500K"(gen-temp=300K,ref-t=500K) and "generate at 500K and thermostat at 
500K"(gen-temp=500K, ref-t=500K)  are OK?

And the latter one is recommended?

Ouyang








At 2017-03-20 21:56:35, "Mark Abraham"  wrote:
>Hi,
>
>Will "generate at 300K but themostat at 500K" take more or less time to
>equilibrate than "generate at 500K and thermostat at 500K"? Both have the
>same desired end state when equilibration is over, so why not start closer
>to it?
>
>Mark
>
>On Mon, Mar 20, 2017 at 2:01 PM YanhuaOuyang <15901283...@163.com> wrote:
>
>> Hi,
>> I plan to run a REMD for a protein in explicit water. The temperature
>> is 300k-500k and there are 40 replicas.
>> I wander that are only the "ref-t" option in the equi_*.mdp files
>> different when equilibration stage ? what about gen-temp option. should I
>> make the gen-temp equal to ref-t (i.e. ref-t=gen-temp=500K)?
>>
>> Best regards,
>> Ouyang
>> --
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[gmx-users] Index is larger than the number of atoms in the trajectory file

2017-03-20 Thread Mahboobeh Eslami

Hi all GMX usersI hope you are wellI have simulated a protein-ligand complex. 
My protein has two calcium ions. I want to use GMXPBSA approach for free energy 
calculation. 
If I remove calcium ions,  I will get following error in the first step of 
MMPBSA calculation:Fatal error:
Index[1673] 1676 is larger than the number of atoms in the
trajectory file (1675). There is a mismatch in the contents
of your -f, -s and/or -n files.How can I solve this problem. please guide me
Thank you so much
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Re: [gmx-users] Regarding Radial Distribution Functions

2017-03-20 Thread Mark Abraham

Hi,

You already chose your data collection rate in your mdp file. Your
correlation time depends  on the physics (no point collecting data more
often than this, so just using nstxout=1 is bogus). And I'm sure google is
your friend for learning about basic concepts of histograms and bin width.

Mark

On Mon, 20 Mar 2017 18:56 Dilip H N  wrote:

> and how it has influence on rdf..??
>
>
>
>    Sent with Mailtrack
> <
> https://mailtrack.io/install?source=signature=en=cy16f01.di...@nitk.edu.in=22
> >
>
> On Mon, Mar 20, 2017 at 11:24 PM, Dilip H N 
> wrote:
>
> > Can u kindly let me knw where can i get the information of collection
> rate
> > and correlation time.??
> >
> >
> >
> >    Sent with Mailtrack
> > <
> https://mailtrack.io/install?source=signature=en=cy16f01.di...@nitk.edu.in=22
> >
> >
> > On Mon, Mar 20, 2017 at 10:54 PM, Mark Abraham  >
> > wrote:
> >
> >> Hi,
> >>
> >> Well gmx rdf has a -bin option for you to get a feel for where your
> >> existing data supports smoothness. But I literally can't know what your
> >> data's correlation time and collection rate are :-)
> >>
> >> Mark
> >>
> >> On Mon, 20 Mar 2017 18:18 Dilip H N  wrote:
> >>
> >> > So where should i look into..?? 1st i made the indexes, than gave gmx
> >> rdf
> >> > command with -f .trr -s .tpr files, and thn output for the rdf...
> >> > What other things should i look for..??
> >> >
> >> >
> >> >
> >> >    Sent with Mailtrack
> >> > <
> >> > https://mailtrack.io/install?source=signature=en
> >> al=cy16f01.di...@nitk.edu.in=22
> >> > >
> >> >
> >> > On Mon, Mar 20, 2017 at 10:41 PM, Mark Abraham <
> >> mark.j.abra...@gmail.com>
> >> > wrote:
> >> >
> >> > > Hi,
> >> > >
> >> > > You're making a histogram. The size of the bins and the number of
> >> > > statistically independent data points in each bin are critical
> >> parameters
> >> > > in how smooth that looks.
> >> > >
> >> > > Mark
> >> > >
> >> > > On Mon, 20 Mar 2017 17:00 Dilip H N 
> >> wrote:
> >> > >
> >> > > > Hello.,
> >> > > > I ran a simultion for 10ns [ steps = 1000, dt = 0.002] and
> whn i
> >> > > index
> >> > > > the file and thn if i plot the rdf , the rdf curves are not
> smooth,
> >> > there
> >> > > > are lot of peaks present, and even after runnig the steps for more
> >> no
> >> > of
> >> > > > steps ie., for 20ns and after tht also my rdf peaks are not so
> >> > > smooth...why
> >> > > > is this so..?? How can i smoothen my curve..??
> >> > > >
> >> > > > --
> >> > > > With Best Regards,
> >> > > >
> >> > > > DILIP.H.N
> >> > > > Research Scholar,
> >> > > > Department of Chemistry, NITK.
> >> > > >
> >> > > >
> >> > > >
> >> > > >
> >> > > >
> >> > > >
> >> > > >    Sent with Mailtrack
> >> > > > <
> >> > > > https://mailtrack.io/install?source=signature=en;
> >> > > referral=cy16f01.di...@nitk.edu.in=22
> >> > > > >
> >> > > > --
> >> > > > 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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> or
> >> > > send a mail to gmx-users-requ...@gromacs.org.
> >> > >
> >> >
> >> >
> >> >
> >> > --
> >> > With Best Regards,
> >> >
> >> > DILIP.H.N
> >> > Research Scholar,
> >> > Department of Chemistry, NITK.
> >> > --
> >> > 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
> >>
> >> * Please search the archive at http://www.gromacs.org/Support
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Re: [gmx-users] Regarding Radial Distribution Functions

2017-03-20 Thread Dilip H N

and how it has influence on rdf..??



   Sent with Mailtrack


On Mon, Mar 20, 2017 at 11:24 PM, Dilip H N 
wrote:

> Can u kindly let me knw where can i get the information of collection rate
> and correlation time.??
>
>
>
>    Sent with Mailtrack
> 
>
> On Mon, Mar 20, 2017 at 10:54 PM, Mark Abraham 
> wrote:
>
>> Hi,
>>
>> Well gmx rdf has a -bin option for you to get a feel for where your
>> existing data supports smoothness. But I literally can't know what your
>> data's correlation time and collection rate are :-)
>>
>> Mark
>>
>> On Mon, 20 Mar 2017 18:18 Dilip H N  wrote:
>>
>> > So where should i look into..?? 1st i made the indexes, than gave gmx
>> rdf
>> > command with -f .trr -s .tpr files, and thn output for the rdf...
>> > What other things should i look for..??
>> >
>> >
>> >
>> >    Sent with Mailtrack
>> > <
>> > https://mailtrack.io/install?source=signature=en
>> al=cy16f01.di...@nitk.edu.in=22
>> > >
>> >
>> > On Mon, Mar 20, 2017 at 10:41 PM, Mark Abraham <
>> mark.j.abra...@gmail.com>
>> > wrote:
>> >
>> > > Hi,
>> > >
>> > > You're making a histogram. The size of the bins and the number of
>> > > statistically independent data points in each bin are critical
>> parameters
>> > > in how smooth that looks.
>> > >
>> > > Mark
>> > >
>> > > On Mon, 20 Mar 2017 17:00 Dilip H N 
>> wrote:
>> > >
>> > > > Hello.,
>> > > > I ran a simultion for 10ns [ steps = 1000, dt = 0.002] and whn i
>> > > index
>> > > > the file and thn if i plot the rdf , the rdf curves are not smooth,
>> > there
>> > > > are lot of peaks present, and even after runnig the steps for more
>> no
>> > of
>> > > > steps ie., for 20ns and after tht also my rdf peaks are not so
>> > > smooth...why
>> > > > is this so..?? How can i smoothen my curve..??
>> > > >
>> > > > --
>> > > > With Best Regards,
>> > > >
>> > > > DILIP.H.N
>> > > > Research Scholar,
>> > > > Department of Chemistry, NITK.
>> > > >
>> > > >
>> > > >
>> > > >
>> > > >
>> > > >
>> > > >    Sent with Mailtrack
>> > > > <
>> > > > https://mailtrack.io/install?source=signature=en;
>> > > referral=cy16f01.di...@nitk.edu.in=22
>> > > > >
>> > > > --
>> > > > 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
>> > Research Scholar,
>> > Department of Chemistry, NITK.
>> > --
>> > 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.
>>
>
>
>
> --
> With Best Regards,
>
> DILIP.H.N
> Research Scholar,
> Department of Chemistry, NITK.
>



-- 
With Best Regards,

DILIP.H.N
Research Scholar,
Department of Chemistry, NITK.
-- 
Gromacs Users mailing list

* Please search the archive at 
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Re: [gmx-users] Regarding Radial Distribution Functions

2017-03-20 Thread Dilip H N

Can u kindly let me knw where can i get the information of collection rate
and correlation time.??



   Sent with Mailtrack


On Mon, Mar 20, 2017 at 10:54 PM, Mark Abraham 
wrote:

> Hi,
>
> Well gmx rdf has a -bin option for you to get a feel for where your
> existing data supports smoothness. But I literally can't know what your
> data's correlation time and collection rate are :-)
>
> Mark
>
> On Mon, 20 Mar 2017 18:18 Dilip H N  wrote:
>
> > So where should i look into..?? 1st i made the indexes, than gave gmx rdf
> > command with -f .trr -s .tpr files, and thn output for the rdf...
> > What other things should i look for..??
> >
> >
> >
> >    Sent with Mailtrack
> > <
> > https://mailtrack.io/install?source=signature=en;
> referral=cy16f01.di...@nitk.edu.in=22
> > >
> >
> > On Mon, Mar 20, 2017 at 10:41 PM, Mark Abraham  >
> > wrote:
> >
> > > Hi,
> > >
> > > You're making a histogram. The size of the bins and the number of
> > > statistically independent data points in each bin are critical
> parameters
> > > in how smooth that looks.
> > >
> > > Mark
> > >
> > > On Mon, 20 Mar 2017 17:00 Dilip H N  wrote:
> > >
> > > > Hello.,
> > > > I ran a simultion for 10ns [ steps = 1000, dt = 0.002] and whn i
> > > index
> > > > the file and thn if i plot the rdf , the rdf curves are not smooth,
> > there
> > > > are lot of peaks present, and even after runnig the steps for more no
> > of
> > > > steps ie., for 20ns and after tht also my rdf peaks are not so
> > > smooth...why
> > > > is this so..?? How can i smoothen my curve..??
> > > >
> > > > --
> > > > With Best Regards,
> > > >
> > > > DILIP.H.N
> > > > Research Scholar,
> > > > Department of Chemistry, NITK.
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >    Sent with Mailtrack
> > > > <
> > > > https://mailtrack.io/install?source=signature=en;
> > > referral=cy16f01.di...@nitk.edu.in=22
> > > > >
> > > > --
> > > > 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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> > > 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
> > Research Scholar,
> > Department of Chemistry, NITK.
> > --
> > 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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> send a mail to gmx-users-requ...@gromacs.org.
>



-- 
With Best Regards,

DILIP.H.N
Research Scholar,
Department of Chemistry, NITK.
-- 
Gromacs Users mailing list

* Please search the archive at 
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Re: [gmx-users] Regarding Radial Distribution Functions

2017-03-20 Thread Mark Abraham

Hi,

Well gmx rdf has a -bin option for you to get a feel for where your
existing data supports smoothness. But I literally can't know what your
data's correlation time and collection rate are :-)

Mark

On Mon, 20 Mar 2017 18:18 Dilip H N  wrote:

> So where should i look into..?? 1st i made the indexes, than gave gmx rdf
> command with -f .trr -s .tpr files, and thn output for the rdf...
> What other things should i look for..??
>
>
>
>    Sent with Mailtrack
> <
> https://mailtrack.io/install?source=signature=en=cy16f01.di...@nitk.edu.in=22
> >
>
> On Mon, Mar 20, 2017 at 10:41 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > You're making a histogram. The size of the bins and the number of
> > statistically independent data points in each bin are critical parameters
> > in how smooth that looks.
> >
> > Mark
> >
> > On Mon, 20 Mar 2017 17:00 Dilip H N  wrote:
> >
> > > Hello.,
> > > I ran a simultion for 10ns [ steps = 1000, dt = 0.002] and whn i
> > index
> > > the file and thn if i plot the rdf , the rdf curves are not smooth,
> there
> > > are lot of peaks present, and even after runnig the steps for more no
> of
> > > steps ie., for 20ns and after tht also my rdf peaks are not so
> > smooth...why
> > > is this so..?? How can i smoothen my curve..??
> > >
> > > --
> > > With Best Regards,
> > >
> > > DILIP.H.N
> > > Research Scholar,
> > > Department of Chemistry, NITK.
> > >
> > >
> > >
> > >
> > >
> > >
> > >    Sent with Mailtrack
> > > <
> > > https://mailtrack.io/install?source=signature=en;
> > referral=cy16f01.di...@nitk.edu.in=22
> > > >
> > > --
> > > 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/
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> --
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>
> DILIP.H.N
> Research Scholar,
> Department of Chemistry, NITK.
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Re: [gmx-users] Regarding Radial Distribution Functions

2017-03-20 Thread Dilip H N

So where should i look into..?? 1st i made the indexes, than gave gmx rdf
command with -f .trr -s .tpr files, and thn output for the rdf...
What other things should i look for..??



   Sent with Mailtrack


On Mon, Mar 20, 2017 at 10:41 PM, Mark Abraham 
wrote:

> Hi,
>
> You're making a histogram. The size of the bins and the number of
> statistically independent data points in each bin are critical parameters
> in how smooth that looks.
>
> Mark
>
> On Mon, 20 Mar 2017 17:00 Dilip H N  wrote:
>
> > Hello.,
> > I ran a simultion for 10ns [ steps = 1000, dt = 0.002] and whn i
> index
> > the file and thn if i plot the rdf , the rdf curves are not smooth, there
> > are lot of peaks present, and even after runnig the steps for more no of
> > steps ie., for 20ns and after tht also my rdf peaks are not so
> smooth...why
> > is this so..?? How can i smoothen my curve..??
> >
> > --
> > With Best Regards,
> >
> > DILIP.H.N
> > Research Scholar,
> > Department of Chemistry, NITK.
> >
> >
> >
> >
> >
> >
> >    Sent with Mailtrack
> > <
> > https://mailtrack.io/install?source=signature=en;
> referral=cy16f01.di...@nitk.edu.in=22
> > >
> > --
> > 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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-- 
With Best Regards,

DILIP.H.N
Research Scholar,
Department of Chemistry, NITK.
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Re: [gmx-users] Pressure and box volume

2017-03-20 Thread Mark Abraham

Hi,

Look at the simulation box volume over time. You can't start making
measurements of pressure at equilibrium until that converges, but
fortunately the volume is less noisy. Then you need a large amount of data
to observe that the average pressure matches the external pressure because
of the massive fluctuations in the former. (Look at a plot of pressure over
time.) Whether that will happen at a desirable volume depends on the
quality of the underlying model.

Mark

On Mon, 20 Mar 2017 16:55 Mishelle Oña  wrote:

> Hello Justin,
>
> Thanks for your response. I made the following steps before the pressure
> error happened:
>
> 1)Built a system of 1 polymer (30 monomer)
>
> 2)Run EM simulation in vaccum
>
> 3) Add solvent (water)
>
> 4) Run a EM simulation with the solvated system
>
> 5) Run a relaxation simulation
>
> 6) Run a NVT simulation
>
> 7) Run NPT simulation (when the problem occured)
>
> It is supposed that NVT simulation stabilizes temperature and it actually
> does. Then NPT simulation is used to stabilize the pressure but this did
> not happend. I run a 500 ps and the a 5000 ps simulation and it still has
> the same pressure of 300 bar aprox.
>
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin
> Lemkul 
> Sent: Monday, March 20, 2017 6:54 AM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Pressure and box volume
>
>
>
> On 3/19/17 8:42 PM, Mishelle Oña wrote:
> > Hello Justin!
> >
> > I was trying to getting down the pressure of my simulation from aprox
> 300 bar to 1 bar. I increased the box volume and now I have 27 bars but my
> density decrease dramatically from 970 to 320 kg/m3. I tried to add more
> water molecules to increase it again but then the pressure scaled up to 300
> bar again. To make a production simulation we should equilibrate the
> parameters of Temperature, Pressure, density and Volume. Should I continue
> playing with the size of the box and the amount of water molecules until I
> get all this parameters acording to the conditions I want or is anything
> else I can do instead?
> >
>
> "Randomly toying with box size and water content" is not a reproducible
> method :)
>
> We're missing a lot of context here, like everything you've done up to this
> point, so it's really hard to comment.  But in general, it is certainly not
> necessary to make all these ad hoc changes.  You may just have to wait a
> while
> for the pressure to stabilize, depending on how far from equilibrium your
> initial state was (and it sounds like it was pretty far from your desired
> value).
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
> [http://mackerell.umaryland.edu/~jalemkul/Images/lemkul_small.jpg]<
> http://mackerell.umaryland.edu/~jalemkul>
>
> Justin A. Lemkul - MacKerell Lab
> mackerell.umaryland.edu
> Welcome to my site! To learn more about me and the work I am doing, please
> use the navigation links above.
>
>
>
>
> ==
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Re: [gmx-users] Regarding Radial Distribution Functions

2017-03-20 Thread Mark Abraham

Hi,

You're making a histogram. The size of the bins and the number of
statistically independent data points in each bin are critical parameters
in how smooth that looks.

Mark

On Mon, 20 Mar 2017 17:00 Dilip H N  wrote:

> Hello.,
> I ran a simultion for 10ns [ steps = 1000, dt = 0.002] and whn i index
> the file and thn if i plot the rdf , the rdf curves are not smooth, there
> are lot of peaks present, and even after runnig the steps for more no of
> steps ie., for 20ns and after tht also my rdf peaks are not so smooth...why
> is this so..?? How can i smoothen my curve..??
>
> --
> With Best Regards,
>
> DILIP.H.N
> Research Scholar,
> Department of Chemistry, NITK.
>
>
>
>
>
>
>    Sent with Mailtrack
> <
> https://mailtrack.io/install?source=signature=en=cy16f01.di...@nitk.edu.in=22
> >
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Re: [gmx-users] Pressure and box volume

2017-03-20 Thread Mishelle Oña

Hello Justin,

Thanks for your response. I made the following steps before the pressure error 
happened:

1)Built a system of 1 polymer (30 monomer)

2)Run EM simulation in vaccum

3) Add solvent (water)

4) Run a EM simulation with the solvated system

5) Run a relaxation simulation

6) Run a NVT simulation

7) Run NPT simulation (when the problem occured)

It is supposed that NVT simulation stabilizes temperature and it actually does. 
Then NPT simulation is used to stabilize the pressure but this did not happend. 
I run a 500 ps and the a 5000 ps simulation and it still has the same pressure 
of 300 bar aprox.

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Justin Lemkul 

Sent: Monday, March 20, 2017 6:54 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Pressure and box volume

On 3/19/17 8:42 PM, Mishelle Oña wrote:
> Hello Justin!
>
> I was trying to getting down the pressure of my simulation from aprox 300 bar 
> to 1 bar. I increased the box volume and now I have 27 bars but my density 
> decrease dramatically from 970 to 320 kg/m3. I tried to add more water 
> molecules to increase it again but then the pressure scaled up to 300 bar 
> again. To make a production simulation we should equilibrate the parameters 
> of Temperature, Pressure, density and Volume. Should I continue playing with 
> the size of the box and the amount of water molecules until I get all this 
> parameters acording to the conditions I want or is anything else I can do 
> instead?
>

"Randomly toying with box size and water content" is not a reproducible method 
:)

We're missing a lot of context here, like everything you've done up to this
point, so it's really hard to comment.  But in general, it is certainly not
necessary to make all these ad hoc changes.  You may just have to wait a while
for the pressure to stabilize, depending on how far from equilibrium your
initial state was (and it sounds like it was pretty far from your desired 
value).

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
[http://mackerell.umaryland.edu/~jalemkul/Images/lemkul_small.jpg]

Justin A. Lemkul - MacKerell Lab
mackerell.umaryland.edu
Welcome to my site! To learn more about me and the work I am doing, please use 
the navigation links above.

==
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[gmx-users] Regarding Radial Distribution Functions

2017-03-20 Thread Dilip H N

Hello.,
I ran a simultion for 10ns [ steps = 1000, dt = 0.002] and whn i index
the file and thn if i plot the rdf , the rdf curves are not smooth, there
are lot of peaks present, and even after runnig the steps for more no of
steps ie., for 20ns and after tht also my rdf peaks are not so smooth...why
is this so..?? How can i smoothen my curve..??

-- 
With Best Regards,

DILIP.H.N
Research Scholar,
Department of Chemistry, NITK.






   Sent with Mailtrack

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Re: [gmx-users] mdp options for REMD

2017-03-20 Thread Mark Abraham

Hi,

Will "generate at 300K but themostat at 500K" take more or less time to
equilibrate than "generate at 500K and thermostat at 500K"? Both have the
same desired end state when equilibration is over, so why not start closer
to it?

Mark

On Mon, Mar 20, 2017 at 2:01 PM YanhuaOuyang <15901283...@163.com> wrote:

> Hi,
> I plan to run a REMD for a protein in explicit water. The temperature
> is 300k-500k and there are 40 replicas.
> I wander that are only the "ref-t" option in the equi_*.mdp files
> different when equilibration stage ? what about gen-temp option. should I
> make the gen-temp equal to ref-t (i.e. ref-t=gen-temp=500K)?
>
> Best regards,
> Ouyang
> --
> Gromacs Users mailing list
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[gmx-users] mdp options for REMD

2017-03-20 Thread YanhuaOuyang

Hi,
I plan to run a REMD for a protein in explicit water. The temperature is 
300k-500k and there are 40 replicas.
I wander that are only the "ref-t" option in the equi_*.mdp files different 
when equilibration stage ? what about gen-temp option. should I make the 
gen-temp equal to ref-t (i.e. ref-t=gen-temp=500K)?

Best regards,
Ouyang
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Re: [gmx-users] topology for charmm

2017-03-20 Thread Justin Lemkul




On 3/20/17 7:13 AM, RAHUL SURESH wrote:

How to reduce param and charge penality while generating stream file?



Large penalties indicate poor similarity with existing groups in the force 
field.  In those cases, you have to manually reparametrize those groups using 
the published CGenFF protocol and the tutorials we have online.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Dihedral drivers and 2D Energy Plot in gromacs

2017-03-20 Thread Justin Lemkul

On 3/20/17 2:50 AM, Devashish_Das wrote:

Thanks for the reply.
The problem now I am facing is, the total energy ( 15960125.0 kJ/mol for 180-180
degree) and dihderal restraint (Its coming like 0.594114 for 180-180 degree).
What I am currently trying is:

1. Take the AIB dipeptide and do minimization in vacuum to get the nearly angle
of Phi-Psi desired (I am doing it for every 10 degree)
2. Add water box manually to the minimized AIB.gro file (For keeping the number
of water molecule exactly same?)
3. Minimize the system again with restraints.
4. remove the restraints from the .top file and use a normal .mdp file for
generating .tpr file
5. Use this tpr and minimized gro file with water to do mdrun -rerun
6. Use gmx energy to calculate "Total Energy" from the rerun.edr and "Dihedral
Restraint" from AIB_water_minimized.edr file
7. Plot the final Energy (= (Total Energy - Dihedral Restraint Energy) - minimum
of the list)

Am I doing this right?

No, you shouldn't be involving water at all, and the manual overlay of the same 
water box on every system is undoubtedly going to cause atomic overlap that 
leads to the bizarre energies.

What you care most about is the relative energetics in vacuum; balancing 
intermolecular interactions is a totally separate issue.

-Justin

On Fri, Mar 17, 2017 at 7:16
PM, > wrote:

Message: 4
Date: Fri, 17 Mar 2017 09:45:21 -0400
From: Justin Lemkul >
To: gmx-us...@gromacs.org 
Subject: Re: [gmx-users] Dihedral drivers and 2D Energy Plot in
gromacs
Message-ID: <85061dd9-acaa-0b50-9eaf-4efb5081d...@vt.edu
>
Content-Type: text/plain; charset=windows-1252; format=flowed

On 3/17/17 1:40 AM, Devashish_Das wrote:
> Hello All,
>
> Presently we are working in generating dihedral drivers for AIB dipeptide
> in gromacs. We would like to create energy contour maps for different phi,
> psi angle for AIB in gromacs. We are unable to create the correct energy
> map vs phi/psi angle of AIB dipeptide during energy minimization step in
> Gromacs.
>
> Our MDP:
> #
> ; Parameters describing what to do, when to stop and what to save
> integrator = cg
> emtol = 1.0
> emstep= 0.01
> nsteps = 5
> #
>
> We retraining the dihedral angles using the following method:
> http://www.gromacs.org/Documentation/How-tos/Dihedral_Restraints
 (*Is this
> the correct way to do this?*)
>
> As clarified Dr Justin Lemkul in a private mail, we need to do the
> following:
>
> * The 2-D energy surface requires several steps.  You need to
> assign dihedral restraints in the topology and relevant .mdp options, and
> minimize the structures with those restrained phi/psi pairs.  You then 
need
> to deactivate the restraints and use mdrun -rerun to recompute the energy
> of the minimized conformation to eliminate the contribution from the
> restraint potential
> (http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy

> >).  Then
> you need to offset the surface to the global minimum (done completely
> outside GROMACS)*
>
> But we are having following trouble:
>
> a)  "*You then need to deactivate the restraints and use mdrun -rerun to
> recompute the energy of the minimized conformation to eliminate the
> contribution from the restraint potential*". How to do this? Which .mdp
> file to be used for *mdrun -rerun*?
>

Anything that's not energy minimization.  Your topology also should either 
not
include the dihedral restraint, or you should extract its contribution from 
the
.edr file and subtract it from the total energy of the system.

> b)  "Then you need to offset the surface to the global minimum (done
> completely outside GROMACS)". Can you provide the required tool name?
>

There isn't one.  This is a trivial scripting exercise.  You assemble the 
2-D
matrix of energy values, find the lowest energy, and apply it as a global 
offset
to all values.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University

Re: [gmx-users] Pressure and box volume

2017-03-20 Thread Justin Lemkul




On 3/19/17 8:42 PM, Mishelle Oña wrote:

Hello Justin!

I was trying to getting down the pressure of my simulation from aprox 300 bar 
to 1 bar. I increased the box volume and now I have 27 bars but my density 
decrease dramatically from 970 to 320 kg/m3. I tried to add more water 
molecules to increase it again but then the pressure scaled up to 300 bar 
again. To make a production simulation we should equilibrate the parameters of 
Temperature, Pressure, density and Volume. Should I continue playing with the 
size of the box and the amount of water molecules until I get all this 
parameters acording to the conditions I want or is anything else I can do 
instead?



"Randomly toying with box size and water content" is not a reproducible method 
:)

We're missing a lot of context here, like everything you've done up to this 
point, so it's really hard to comment.  But in general, it is certainly not 
necessary to make all these ad hoc changes.  You may just have to wait a while 
for the pressure to stabilize, depending on how far from equilibrium your 
initial state was (and it sounds like it was pretty far from your desired value).


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Pressure in NPT simulation

2017-03-20 Thread Justin Lemkul




On 3/19/17 3:34 PM, Mishelle Oña wrote:

Hello Justin, thanks for your help. The simulation has 250 steps (5000ps).



Depending on what your polymer is and how it behaves (entanglement, etc) it may 
take a long time to converge.  For a very simple system, 5 ns should be enough. 
For a polymer, I don't know what you should expect.


-Justin


Mishelle



From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Justin Lemkul 

Sent: Sunday, March 19, 2017 2:20 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Pressure in NPT simulation



On 3/19/17 3:17 PM, Mishelle Oña wrote:

Hello,

I have a question concerning pressure. I runned a NPT simulation with the 
following parameters:

; Pressure coupling
Pcoupl   = Berendsen
Pcoupltype   = Isotropic
tau_p= 1.01325


This is a rather odd value of tau_p.  Remember this is time, not bar.


compressibility  = 4.5e-5
ref_p= 1.01325
When analyzing the average pressure using g_energy I got this results:
Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Potential   -1286139.9363.247   -65.2445  (kJ/mol)
Kinetic En. 24189.21.4242.381   -6.10124  (kJ/mol)
Total Energy-104424 11440.485   -71.3457  (kJ/mol)
Temperature 300.544  0.0183.01152 -0.0758065  (K)
Pressure323.536   0.65244.361   -3.94119  (bar)

I wonder why the simulation cannot descent to the ref_p value. It is a system 
of a polymer in a box full of water.
 Thanks for the answer and help.


How long was the simulation?  Have you read
http://www.gromacs.org/Documentation/Terminology/Pressure and/or any of the
million or so posts where people wonder about weird values of pressure? :)

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
[http://mackerell.umaryland.edu/~jalemkul/Images/lemkul_small.jpg]

Justin A. Lemkul - MacKerell Lab
mackerell.umaryland.edu
Welcome to my site! To learn more about me and the work I am doing, please use 
the navigation links above.



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==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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[gmx-users] topology for charmm

2017-03-20 Thread RAHUL SURESH

How to reduce param and charge penality while generating stream file?

-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
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Re: [gmx-users] How to access recent discussion on gmx-user list?

2017-03-20 Thread Amir Zeb

Thanks a lot Das,

You really solved my problem.

Amir

On Mon, Mar 20, 2017 at 3:06 AM, Devashish_Das 
wrote:

> Please use this link:
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/
>
> On Mon, Mar 20, 2017 at 3:01 PM, Amir Zeb  wrote:
>
> > Hello folks,
> >
> > I want to access the updated discussion on gmx-user list but mostly I'm
> > getting into this page while searching for "
> > https://www.mail-archive.com/gmx-users@gromacs.org/index.html;, This
> page
> > gives me very early discussion like 2013 and data I could find after
> 2103.
> > Please let me know the link to access the updated discussion.
> >
> > Thanks
> >
> > Amir
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
>
>
>
> --
>
> Regards,
>
> Devashish Das
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Re: [gmx-users] How to access recent discussion on gmx-user list?

2017-03-20 Thread Devashish_Das

Please use this link:
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/

On Mon, Mar 20, 2017 at 3:01 PM, Amir Zeb  wrote:

> Hello folks,
>
> I want to access the updated discussion on gmx-user list but mostly I'm
> getting into this page while searching for "
> https://www.mail-archive.com/gmx-users@gromacs.org/index.html;, This page
> gives me very early discussion like 2013 and data I could find after 2103.
> Please let me know the link to access the updated discussion.
>
> Thanks
>
> Amir
> --
> Gromacs Users mailing list
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>



-- 

Regards,

Devashish Das
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[gmx-users] How to access recent discussion on gmx-user list?

2017-03-20 Thread Amir Zeb

Hello folks,

I want to access the updated discussion on gmx-user list but mostly I'm
getting into this page while searching for "
https://www.mail-archive.com/gmx-users@gromacs.org/index.html;, This page
gives me very early discussion like 2013 and data I could find after 2103.
Please let me know the link to access the updated discussion.

Thanks

Amir
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Re: [gmx-users] Dihedral drivers and 2D Energy Plot in gromacs

2017-03-20 Thread Devashish_Das

Thanks for the reply.
The problem now I am facing is, the total energy ( 15960125.0 kJ/mol for
180-180 degree) and dihderal restraint (Its coming like 0.594114 for
180-180 degree).
What I am currently trying is:

1. Take the AIB dipeptide and do minimization in vacuum to get the nearly
angle of Phi-Psi desired (I am doing it for every 10 degree)
2. Add water box manually to the minimized AIB.gro file (For keeping the
number of water molecule exactly same?)
3. Minimize the system again with restraints.
4. remove the restraints from the .top file and use a normal .mdp file for
generating .tpr file
5. Use this tpr and minimized gro file with water to do mdrun -rerun
6. Use gmx energy to calculate "Total Energy" from the rerun.edr and
"Dihedral Restraint" from AIB_water_minimized.edr file
7. Plot the final Energy (= (Total Energy - Dihedral Restraint Energy) -
minimum of the list)

Am I doing this right?


On Fri, Mar 17, 2017 at 7:16 PM, <
gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote:

> Message: 4
> Date: Fri, 17 Mar 2017 09:45:21 -0400
> From: Justin Lemkul 
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Dihedral drivers and 2D Energy Plot in
> gromacs
> Message-ID: <85061dd9-acaa-0b50-9eaf-4efb5081d...@vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 3/17/17 1:40 AM, Devashish_Das wrote:
> > Hello All,
> >
> > Presently we are working in generating dihedral drivers for AIB dipeptide
> > in gromacs. We would like to create energy contour maps for different
> phi,
> > psi angle for AIB in gromacs. We are unable to create the correct energy
> > map vs phi/psi angle of AIB dipeptide during energy minimization step in
> > Gromacs.
> >
> > Our MDP:
> > #
> > ; Parameters describing what to do, when to stop and what to save
> > integrator = cg
> > emtol = 1.0
> > emstep= 0.01
> > nsteps = 5
> > #
> >
> > We retraining the dihedral angles using the following method:
> > http://www.gromacs.org/Documentation/How-tos/Dihedral_Restraints (*Is
> this
> > the correct way to do this?*)
> >
> > As clarified Dr Justin Lemkul in a private mail, we need to do the
> > following:
> >
> > * The 2-D energy surface requires several steps.  You need to
> > assign dihedral restraints in the topology and relevant .mdp options, and
> > minimize the structures with those restrained phi/psi pairs.  You then
> need
> > to deactivate the restraints and use mdrun -rerun to recompute the energy
> > of the minimized conformation to eliminate the contribution from the
> > restraint potential
> > (http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy
> > ).
> Then
> > you need to offset the surface to the global minimum (done completely
> > outside GROMACS)*
> >
> > But we are having following trouble:
> >
> > a)  "*You then need to deactivate the restraints and use mdrun -rerun to
> > recompute the energy of the minimized conformation to eliminate the
> > contribution from the restraint potential*". How to do this? Which .mdp
> > file to be used for *mdrun -rerun*?
> >
>
> Anything that's not energy minimization.  Your topology also should either
> not
> include the dihedral restraint, or you should extract its contribution
> from the
> .edr file and subtract it from the total energy of the system.
>
> > b)  "Then you need to offset the surface to the global minimum (done
> > completely outside GROMACS)". Can you provide the required tool name?
> >
>
> There isn't one.  This is a trivial scripting exercise.  You assemble the
> 2-D
> matrix of energy values, find the lowest energy, and apply it as a global
> offset
> to all values.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==



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-- 

Thanks & Regards,

Devashish Das
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[gmx-users] Regarding extending simulations

Re: [gmx-users] mdp options for REMD

[gmx-users] Index is larger than the number of atoms in the trajectory file

Re: [gmx-users] Regarding Radial Distribution Functions

Re: [gmx-users] Regarding Radial Distribution Functions

Re: [gmx-users] Regarding Radial Distribution Functions

Re: [gmx-users] Regarding Radial Distribution Functions

Re: [gmx-users] Regarding Radial Distribution Functions

Re: [gmx-users] Pressure and box volume

Re: [gmx-users] Regarding Radial Distribution Functions

Re: [gmx-users] Pressure and box volume

[gmx-users] Regarding Radial Distribution Functions

Re: [gmx-users] mdp options for REMD

[gmx-users] mdp options for REMD

Re: [gmx-users] topology for charmm

Re: [gmx-users] Dihedral drivers and 2D Energy Plot in gromacs

Re: [gmx-users] Pressure and box volume

Re: [gmx-users] Pressure in NPT simulation

[gmx-users] topology for charmm

Re: [gmx-users] How to access recent discussion on gmx-user list?

Re: [gmx-users] How to access recent discussion on gmx-user list?

[gmx-users] How to access recent discussion on gmx-user list?

Re: [gmx-users] Dihedral drivers and 2D Energy Plot in gromacs

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