Re: [gmx-users] Re : WARNING no output error while dumping structures with trjconv from MD.trr

[Justin Lemkul]

On 5/21/16 9:47 AM, Antara mazumdar wrote:

Dear Sir,

The MD.trr i expect to be having 382ns of data as is mentioned in the log
file and MD.xtc that was generated alongwith MD.trr when the simulation
ran  has 382ns.

However, MD.trr has problems in giving output beyond 25ns. Could it be
corruption of frames or something?


gmx check will tell you this.

-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

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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

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

[gmx-users] Re : WARNING no output error while dumping structures with trjconv from MD.trr

[Antara mazumdar]

Dear Sir,

The MD.trr i expect to be having 382ns of data as is mentioned in the log
file and MD.xtc that was generated alongwith MD.trr when the simulation
ran  has 382ns.

However, MD.trr has problems in giving output beyond 25ns. Could it be
corruption of frames or something?
Kind Regards,
Antara

--
Junior research fellow(project)
Systems biology group
CSIR-Institute of Genomics & Integrative Biology
South Campus
New Delhi -  110020
M : +91-9717970040
--
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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

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

Re: [gmx-users] Protein-membrane simulation error.

[Justin Lemkul]

On 5/20/16 6:28 PM, BIJENDRA KHADKA wrote:

Hello,
I received the following error while trying to run "Adding ion" step during
Protein-membrane simulation. Any advice or suggestions will be greatly
appreciated.



You need to tell us all the steps you have taken prior to this point, otherwise 
we're just guessing, which is productive for no one.  In general, you've 
generated a topology that calls for non-existent force field parameters, so 
either you're mixing and matching force fields or you've constructed a force 
field incorrectly.


-Justin



ERROR:
Command line:
  gmx grompp -f ions.mdp -c system_box_sol.gro -p topol.top -o ions.tpr


NOTE 1 [file ions.mdp, line 17]:
  ions.mdp did not specify a value for the .mdp option "cutoff-scheme".
  Probably it was first intended for use with GROMACS before 4.6. In 4.6,
  the Verlet scheme was introduced, but the group scheme was still the
  default. The default is now the Verlet scheme, so you will observe
  different behaviour.


Back Off! I just backed up mdout.mdp to ./#mdout.mdp.11#

NOTE 2 [file ions.mdp]:
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
  that with the Verlet scheme, nstlist has no effect on the accuracy of
  your simulation.

Setting the LD random seed to 1335440429
Generated 968 of the 2016 non-bonded parameter combinations

ERROR 1 [file topol.top, line 765]:
  No default Proper Dih. types


ERROR 2 [file topol.top, line 766]:
  No default Proper Dih. types


ERROR 3 [file topol.top, line 768]:
  No default Proper Dih. types


ERROR 4 [file topol.top, line 769]:
  No default Proper Dih. types


ERROR 5 [file topol.top, line 770]:
  No default Proper Dih. types


ERROR 6 [file topol.top, line 771]:
  No default Proper Dih. types


ERROR 7 [file topol.top, line 772]:
  No default Proper Dih. types


ERROR 8 [file topol.top, line 773]:
  No default Proper Dih. types


ERROR 9 [file topol.top, line 774]:
  No default Proper Dih. types


ERROR 10 [file topol.top, line 776]:
  No default Proper Dih. types


ERROR 11 [file topol.top, line 777]:
  No default Proper Dih. types


ERROR 12 [file topol.top, line 778]:
  No default Proper Dih. types


ERROR 13 [file topol.top, line 779]:
  No default Proper Dih. types


ERROR 14 [file topol.top, line 780]:
  No default Proper Dih. types


ERROR 15 [file topol.top, line 781]:
  No default Proper Dih. types


ERROR 16 [file topol.top, line 782]:
  No default Proper Dih. types


ERROR 17 [file topol.top, line 784]:
  No default Proper Dih. types


ERROR 18 [file topol.top, line 785]:
  No default Proper Dih. types


ERROR 19 [file topol.top, line 786]:
  No default Proper Dih. types


ERROR 20 [file topol.top, line 787]:
  No default Proper Dih. types


ERROR 21 [file topol.top, line 789]:
  No default Proper Dih. types


ERROR 22 [file topol.top, line 790]:
  No default Proper Dih. types


ERROR 23 [file topol.top, line 792]:
  No default Proper Dih. types


ERROR 24 [file topol.top, line 793]:
  No default Proper Dih. types


ERROR 25 [file topol.top, line 794]:
  No default Proper Dih. types


ERROR 26 [file topol.top, line 795]:
  No default Proper Dih. types


ERROR 27 [file topol.top, line 797]:
  No default Proper Dih. types


ERROR 28 [file topol.top, line 798]:
  No default Proper Dih. types


ERROR 29 [file topol.top, line 800]:
  No default Proper Dih. types


ERROR 30 [file topol.top, line 801]:
  No default Proper Dih. types


ERROR 31 [file topol.top, line 802]:
  No default Proper Dih. types


ERROR 32 [file topol.top, line 803]:
  No default Proper Dih. types


ERROR 33 [file topol.top, line 805]:
  No default Proper Dih. types


ERROR 34 [file topol.top, line 806]:
  No default Proper Dih. types


ERROR 35 [file topol.top, line 808]:
  No default Proper Dih. types


ERROR 36 [file topol.top, line 809]:
  No default Proper Dih. types


ERROR 37 [file topol.top, line 810]:
  No default Proper Dih. types


ERROR 38 [file topol.top, line 811]:
  No default Proper Dih. types


ERROR 39 [file topol.top, line 813]:
  No default Proper Dih. types


ERROR 40 [file topol.top, line 814]:
  No default Proper Dih. types


ERROR 41 [file topol.top, line 816]:
  No default Proper Dih. types


ERROR 42 [file topol.top, line 817]:
  No default Proper Dih. types


ERROR 43 [file topol.top, line 818]:
  No default Proper Dih. types


ERROR 44 [file topol.top, line 819]:
  No default Proper Dih. types


ERROR 45 [file topol.top, line 821]:
  No default Proper Dih. types


ERROR 46 [file topol.top, line 822]:
  No default Proper Dih. types


ERROR 47 [file topol.top, line 823]:
  No default Proper Dih. types


ERROR 48 [file topol.top, line 824]:
  No default Proper Dih. types


ERROR 49 [file topol.top, line 825]:
  No default Proper Dih. types


ERROR 50 [file topol.top, line 826]:
  No default Proper Dih. types


ERROR 51 [file topol.top, line 827]:
  No default Proper Dih. types


ERROR 52 [file topol.top, line 829]:
  No default Proper Dih. types


ERROR 53 [file 

Re: [gmx-users] help required in plotting percentage of protein in contact with membrane vs time

[Justin Lemkul]

On 5/21/16 8:54 AM, Antara mazumdar wrote:

Dear Gromacs users,

  I have a membrane protein simulation performed with gromacs 4.6. I have
calculated the minimum distance of protein residues from upper leaflet of
the lipid bilayer. I also have the time wise atom pair contacts as an
output.
The following command i used :

g_mindist -f SYSTEM_FIT_SIM4_DT100.xtc -s MD_4_NOWATER.tpr -n ../index.ndx
-d 0.7 -o atompair -on numcontact -od mindist.xvg

The atom pair out output i got was as follow :

.00e+00  2412281928
1.00e+02  1630266151
2.00e+02  1630266151
3.00e+02  2410284225
4.00e+02  2412284225
5.00e+02  2412284225
6.00e+02  2410284225
7.00e+02  2410284225
8.00e+02  2410284225
9.00e+02  2410284225
1.00e+03  2405284225
1.10e+03  2411281928
1.20e+03  2412284225
1.30e+03  2332285163
1.40e+03  2411284225
1.50e+03  2410284225
1.60e+03  1555264261
1.70e+03  1555264261
1.80e+03  1555264261
1.90e+03  1554266958
2.00e+03  2389266958
2.10e+03  2411285163
2.20e+03  2412285163
2.30e+03  2412285163
2.40e+03  2410285163
2.50e+03  2410285163
2.60e+03  2412285163


 I now need to find out time wise percentage of protein covering the
membrane. I want to know for instance, at time t=0ns, what is the protein
coverage % and similarly for the entire trajectory i want to calculate this.


Kindly suggest something!!



The solution was already suggested to you - calculated the buried surface area. 
You can express that as a fraction of the protein's surface area.


-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

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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

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

[gmx-users] help required in plotting percentage of protein in contact with membrane vs time

[Antara mazumdar]

Dear Gromacs users,

  I have a membrane protein simulation performed with gromacs 4.6. I have
calculated the minimum distance of protein residues from upper leaflet of
the lipid bilayer. I also have the time wise atom pair contacts as an
output.
The following command i used :

g_mindist -f SYSTEM_FIT_SIM4_DT100.xtc -s MD_4_NOWATER.tpr -n ../index.ndx
-d 0.7 -o atompair -on numcontact -od mindist.xvg

The atom pair out output i got was as follow :

.00e+00  2412281928
1.00e+02  1630266151
2.00e+02  1630266151
3.00e+02  2410284225
4.00e+02  2412284225
5.00e+02  2412284225
6.00e+02  2410284225
7.00e+02  2410284225
8.00e+02  2410284225
9.00e+02  2410284225
1.00e+03  2405284225
1.10e+03  2411281928
1.20e+03  2412284225
1.30e+03  2332285163
1.40e+03  2411284225
1.50e+03  2410284225
1.60e+03  1555264261
1.70e+03  1555264261
1.80e+03  1555264261
1.90e+03  1554266958
2.00e+03  2389266958
2.10e+03  2411285163
2.20e+03  2412285163
2.30e+03  2412285163
2.40e+03  2410285163
2.50e+03  2410285163
2.60e+03  2412285163


 I now need to find out time wise percentage of protein covering the
membrane. I want to know for instance, at time t=0ns, what is the protein
coverage % and similarly for the entire trajectory i want to calculate this.


Kindly suggest something!!

Kind Regards,
Antara

--
Junior research fellow(project)
Systems biology group
CSIR-Institute of Genomics & Integrative Biology
South Campus
New Delhi -  110020
M : +91-9717970040
--
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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

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

Re: [gmx-users] WARNING no output error while dumping structures with trjconv from MD.trr

[Tsjerk Wassenaar]

Oh, you don't want to dump one frame! You want the frames beyond 25 ns. So
don't use -dump at all. You'll only get one frame though, using a spacing
of 1 ns.

Cheers,

Tsjerk
On May 21, 2016 13:53, "Tsjerk Wassenaar"  wrote:

> Hi Antara,
>
> You indicate you want the frame at 27ns (-dump 27000), but that's not in
> the trajectory. The suggestion is to ask for a frame that is in, like -dump
> 25290
>
> Cheers,
>
> Tsjerk
> On May 21, 2016 13:09, "Antara mazumdar"  wrote:
>
> Dear gromacs users,
>
>I was trying to dump structures from MD.trr using trjconv. The MD.trr
> has 0ns to 382ns of data. (i checked the MD.log file also).  However, when
> i try to dump structures beyond 25ns, with the following command :
> *gmx trjconv mpi -f MD.trr -dump 27000.000 -dt 1000 -s MD.tpr -b 2.000*
>
>
> *it gives the following error :WARNING no output, last frame read at
> t=25290*
>
> I have also tried to check with gmxcheck but it only runs till 20ns.
>
> trjconv and or gmxcheck did not give any error with MD.xtc which was
> generated during the simulation.
>
> I require the MD.trr as i  need velocity and force information for my
> analysis.
>
> Kindly suggest something!!
> Kind Regards,
> Antara
>
> --
> Junior research fellow(project)
> Systems biology group
> CSIR-Institute of Genomics & Integrative Biology
> South Campus
> New Delhi -  110020
> M : +91-9717970040
> --
> --
> 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.

Re: [gmx-users] WARNING no output error while dumping structures with trjconv from MD.trr

[Tsjerk Wassenaar]

Hi Antara,

You indicate you want the frame at 27ns (-dump 27000), but that's not in
the trajectory. The suggestion is to ask for a frame that is in, like -dump
25290

Cheers,

Tsjerk
On May 21, 2016 13:09, "Antara mazumdar"  wrote:

Dear gromacs users,

   I was trying to dump structures from MD.trr using trjconv. The MD.trr
has 0ns to 382ns of data. (i checked the MD.log file also).  However, when
i try to dump structures beyond 25ns, with the following command :
*gmx trjconv mpi -f MD.trr -dump 27000.000 -dt 1000 -s MD.tpr -b 2.000*


*it gives the following error :WARNING no output, last frame read at
t=25290*

I have also tried to check with gmxcheck but it only runs till 20ns.

trjconv and or gmxcheck did not give any error with MD.xtc which was
generated during the simulation.

I require the MD.trr as i  need velocity and force information for my
analysis.

Kindly suggest something!!
Kind Regards,
Antara

--
Junior research fellow(project)
Systems biology group
CSIR-Institute of Genomics & Integrative Biology
South Campus
New Delhi -  110020
M : +91-9717970040
--
--
Gromacs Users mailing list

* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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

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

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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

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

[gmx-users] WARNING no output error while dumping structures with trjconv from MD.trr

[Antara mazumdar]

Dear gromacs users,

   I was trying to dump structures from MD.trr using trjconv. The MD.trr
has 0ns to 382ns of data. (i checked the MD.log file also).  However, when
i try to dump structures beyond 25ns, with the following command :
*gmx trjconv mpi -f MD.trr -dump 27000.000 -dt 1000 -s MD.tpr -b 2.000*


*it gives the following error :WARNING no output, last frame read at
t=25290*

I have also tried to check with gmxcheck but it only runs till 20ns.

trjconv and or gmxcheck did not give any error with MD.xtc which was
generated during the simulation.

I require the MD.trr as i  need velocity and force information for my
analysis.

Kindly suggest something!!
Kind Regards,
Antara

--
Junior research fellow(project)
Systems biology group
CSIR-Institute of Genomics & Integrative Biology
South Campus
New Delhi -  110020
M : +91-9717970040
--
-- 
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.