[gmx-users] Basic question about command line (Mohammad Madani)

Teslim Olayiwola olayiwolateslim9 at gmail.com
Tue Apr 14 10:35:20 CEST 2020


Hi Mohammed Madani,

Your command is missing the group as mentioned in the error message. While
correct for periodic error, you should ensure that you extract (that's if
your top/file has more than one groups) the appropriate group (not system)
from the production file (xtc) by using trjconv option. After extracting
with trj, you can regenerate the tpr file for the select groups. After
doing this, you can then use the following command

gmxi clustsize -f file.nojump.mol.xtc -n group.ndx -s group.tpr -mol yes
-cut 0.35 -pbc yes

On Tue, 14 Apr 2020 at 11:09, <
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:

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> Today's Topics:
>
>    1. Basic question about command line (Mohammad Madani)
>    2. Basic question about command line (Mohammad Madani)
>    3. Re: Replica exchange probabilities beyond version 2016 (G?l Zerze)
>    4. How to solve the "LINCS WARNING" problem (???)
>    5. Re: How to solve the "LINCS WARNING" problem (Yu Du)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 13 Apr 2020 22:03:07 -0400
> From: Mohammad Madani <mohammad.madani at uconn.edu>
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>,
>         "gromacs.org_gmx-users at maillist.sys.kth.se"
>         <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: [gmx-users] Basic question about command line
> Message-ID:
>         <
> CABaRwomJ3AV7nFPr4cJNbqThWeEBL9wGBrMhWTAu2yEJoxX6-A at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Dear all
> Hi,
> I have a basic question about the using the gromacs.
> I want to use gmx cluster for clustering. I use the cluster hpc.
> When I run the this command:
> gmx cluster -f *.trr -s *.gro -g *.log -clid *.xvg
> I receive the error that I should select the group for least rmsd.
> Could you please help me how can I add this part to the command line?
> Can I do this??
>
> Many thanks
>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 13 Apr 2020 22:03:07 -0400
> From: Mohammad Madani <mohammad.madani at uconn.edu>
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>,
>         "gromacs.org_gmx-users at maillist.sys.kth.se"
>         <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: [gmx-users] Basic question about command line
> Message-ID:
>         <
> CABaRwomJ3AV7nFPr4cJNbqThWeEBL9wGBrMhWTAu2yEJoxX6-A at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Dear all
> Hi,
> I have a basic question about the using the gromacs.
> I want to use gmx cluster for clustering. I use the cluster hpc.
> When I run the this command:
> gmx cluster -f *.trr -s *.gro -g *.log -clid *.xvg
> I receive the error that I should select the group for least rmsd.
> Could you please help me how can I add this part to the command line?
> Can I do this??
>
> Many thanks
>
>
> ------------------------------
>
> Message: 3
> Date: Mon, 13 Apr 2020 22:55:35 -0400
> From: G?l Zerze <h.gul.ozer at gmail.com>
> To: gmx-users at gromacs.org, pganguly at chem.ucsb.edu
> Subject: Re: [gmx-users] Replica exchange probabilities beyond version
>         2016
> Message-ID:
>         <CAD-f+dnsCrsQfPiSH4HK+hEXJvF7ZVw5=
> 6t8zvBHHpgN_w1WZQ at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi Pritam,
>
> Did you check your energy fluctuations? Looks like you are using NH
> thermostat, you might be suffering from the interaction of NH thermostat
> oscillations with resonance modes in the system, which makes energy
> fluctuations substantially larger (compared to fluctuations with NH in
> older versions of Gromacs). As a result of amplified fluctuations, you have
> higher exchange probability. See here for a previous relevant exchange:
> https://redmine.gromacs.org/issues/2904 For my system, making tau_t=10
> helped to recover the old behavior.
>
> Best,
> G?l
> *--*
> *G?l H. Zerze*
> Postdoctoral Research Associate
>
> Chemical and Biological Engineering
> Princeton University
> http://pablonet.princeton.edu/
>
>
>
> On Mon, Apr 13, 2020 at 8:01 PM Pritam Ganguly <pganguly at chem.ucsb.edu>
> wrote:
>
> > Hello,
> >
> > I have noticed that the average exchange probability for a replica
> > exchange run increases significantly if I use Gromacs versions 2018, as
> > compared to versions 2016 or earlier. I have tested that by simulating
> > the same system with versions 2016.4 and 2018.3 and the average
> > probabilities I find are:
> >
> > Version 2016.4:
> >
> > Replica exchange statistics
> > Repl  1666 attempts, 833 odd, 833 even
> > Repl  average probabilities:
> > Repl     0    1    2    3    4    5    6    7    8    9   10 11 12
> > 13   14   15   16   17   18   19   20   21   22   23 24 25   26   27
> > 28   29   30   31   32   33   34   35   36 37 38   39   40   41   42
> > 43   44   45   46   47   48   49 50 51   52   53   54   55   56   57
> > 58   59   60   61   62 63
> > Repl      .29  .33  .29  .30  .28  .30  .30  .29  .29  .29  .30 .26
> > .29  .30  .28  .29  .26  .26  .29  .28  .26  .27  .27  .27 .27  .28
> > .26  .27  .26  .25  .27  .25  .26  .27  .25  .24  .25 .26  .27  .25
> > .27  .26  .26  .26  .25  .26  .26  .24  .25  .27 .26  .27  .26  .25
> > .27  .27  .28  .26  .27  .26  .27  .27  .28
> >
> >
> > Version 2018.3:
> >
> > Replica exchange statistics
> > Repl  1666 attempts, 833 odd, 833 even
> > Repl  average probabilities:
> > Repl     0    1    2    3    4    5    6    7    8    9   10 11 12
> > 13   14   15   16   17   18   19   20   21   22   23 24 25   26   27
> > 28   29   30   31   32   33   34   35   36 37 38   39   40   41   42
> > 43   44   45   46   47   48   49 50 51   52   53   54   55   56   57
> > 58   59   60   61   62 63
> > Repl      .39  .39  .37  .42  .38  .38  .39  .36  .36  .38  .40 .39
> > .40  .39  .37  .35  .40  .39  .35  .38  .40  .35  .38  .35 .36  .35
> > .36  .36  .38  .36  .37  .36  .35  .36  .36  .37  .35 .35  .35  .37
> > .37  .35  .37  .36  .37  .34  .36  .38  .38  .38 .35  .37  .36  .39
> > .36  .40  .38  .38  .40  .36  .37  .36  .33
> >
> > These are test runs for 5 ns with exchange frequencies of 3 ps. I have
> > used the same input parameters for both of these runs (mdp is attached).
> > I actually observed this with many other systems and I was looking for
> > any relevant gromacs release note for versions 2018 or beyond related to
> > the replica exchange algorithm or the way the energies are calculated,
> > but I could not figure it out.
> >
> > Regards,
> >
> > Pritam
> >
> > --
> > Pritam Ganguly
> > Department of Chemistry and Biochemistry
> > University of California at Santa Barbara
> > Santa Barbara, CA, USA 93106
> >
> > Office: PSBN 3606
> > Phone: +1-805-893-2767
> > http://people.chem.ucsb.edu/ganguly/pritam
> >
> > --
> > 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-request at gromacs.org.
>
>
> ------------------------------
>
> Message: 4
> Date: Tue, 14 Apr 2020 15:32:37 +0900
> From: ??? <byunjy0614 at gmail.com>
> To: gmx-users at gromacs.org
> Subject: [gmx-users] How to solve the "LINCS WARNING" problem
> Message-ID: <910FFB5A-B5EE-4EF0-8399-E47AB90034D2 at gmail.com>
> Content-Type: text/plain;       charset=utf-8
>
> Dear GROMACS users,
>
> Since I have run the nvt  and npt processes for the protein-ligand
> interaction, I met the the warning messages below
>
> Step 231785, time 463.57 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.000176, max 0.003912 (between atoms 3035 and 3037)
> bonds that rotated more than 30 degrees:
> atom 1 atom 2  angle  previous, current, constraint length
>    3035   3036   34.0    0.1090   0.1087      0.1090
>
> ?.
>
> Step 231825, time 463.65 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 1840.719238, max 48122.035156 (between atoms 3028 and 3029)
> bonds that rotated more than 30 degrees:
> atom 1 atom 2  angle  previous, current, constraint length
>    3024   3025   90.0    0.1090   0.1236      0.1090
>    3026   3027  100.8    0.1090   6.6242      0.1090
>    3028   3029  162.5    1.7683 5245.4102      0.1090
>    3033   3034  106.7    0.1090 426.5654      0.1090
>    3035   3037   90.0    0.3851   0.7991      0.1090
>    3038   3039   90.0    0.6045   0.4497      0.1090
>    3038   3040   90.0    0.1123   0.2833      0.1090
>    3041   3042   59.0    0.1020   0.1020      0.1020
> Wrote pdb files with previous and current coordinates
>
> Step 231826, time 463.652 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 191384000.000000, max 4098777344.000000 (between atoms 3033 and 3034)
> bonds that rotated more than 30 degrees:
> atom 1 atom 2  angle  previous, current, constraint length
>    1423   1424  140.4    0.1000 503.9983      0.1000
>    3024   3025   61.1    0.1236 223337872.0000      0.1090
>    3026   3027  168.8    6.6242 149263.5000      0.1090
>    3028   3029  165.8  5245.4102 263929.4375      0.1090
>    3031   3032  116.2    0.1090 223428336.0000      0.1090
>    3033   3034  179.9  426.5654 446766720.0000      0.1090
>    3035   3036   35.3   29.6105 831.0708      0.1090
>    3035   3037  102.9    0.7991 775.3371      0.1090
>    3038   3039   90.0    0.4497   0.6355      0.1090
>    3038   3040   47.7    0.2833   0.1111      0.1090
> step 231826: One or more water molecules can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
>
> So I checked the my input configuration. the 3035, 3028, 3035 atoms are
> ligand C atoms and the 3037, 3029, 3034 atoms are the ligand H atoms.
> Why does the LINCS warning      occurs? and How I solve this problem?
>
> Many Thanks
>
> Jinyoung
>
> ------------------------------
>
> Message: 5
> Date: Tue, 14 Apr 2020 08:08:20 +0000
> From: Yu Du <ydu-sci at outlook.com>
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] How to solve the "LINCS WARNING" problem
> Message-ID:
>         <
> SL2PR04MB30336C02709B0CDE69A04AF1E0DA0 at SL2PR04MB3033.apcprd04.prod.outlook.com
> >
>
> Content-Type: text/plain; charset="ks_c_5601-1987"
>
> Hi Jinyoung,
>
> I guess that the LINCS WARNING you encountered maybe came from hiden
> errors in the configuration of either protein or ligand OR more directly
> from the ligand's topology. You need to carefully check the configuration
> of protein and ligand, e.g. side chain goes through benzene ring.
>
> After a careful check, If you want more suggestion, you need to provide
> some details of the generation of ligand's topology.
>
> Du, Yu
> PhD Student,
> Shanghai Institute of Organic Chemistry
> 345 Ling Ling Rd., Shanghai, China.
> Zip: 200032, Tel: (86) 021 5492 5275
> ________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of ??? <
> byunjy0614 at gmail.com>
> Sent: Tuesday, April 14, 2020 14:32
> To: gmx-users at gromacs.org <gmx-users at gromacs.org>
> Subject: [gmx-users] How to solve the "LINCS WARNING" problem
>
> Dear GROMACS users,
>
> Since I have run the nvt  and npt processes for the protein-ligand
> interaction, I met the the warning messages below
>
> Step 231785, time 463.57 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.000176, max 0.003912 (between atoms 3035 and 3037)
> bonds that rotated more than 30 degrees:
> atom 1 atom 2  angle  previous, current, constraint length
>    3035   3036   34.0    0.1090   0.1087      0.1090
>
> ?.
>
> Step 231825, time 463.65 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 1840.719238, max 48122.035156 (between atoms 3028 and 3029)
> bonds that rotated more than 30 degrees:
> atom 1 atom 2  angle  previous, current, constraint length
>    3024   3025   90.0    0.1090   0.1236      0.1090
>    3026   3027  100.8    0.1090   6.6242      0.1090
>    3028   3029  162.5    1.7683 5245.4102      0.1090
>    3033   3034  106.7    0.1090 426.5654      0.1090
>    3035   3037   90.0    0.3851   0.7991      0.1090
>    3038   3039   90.0    0.6045   0.4497      0.1090
>    3038   3040   90.0    0.1123   0.2833      0.1090
>    3041   3042   59.0    0.1020   0.1020      0.1020
> Wrote pdb files with previous and current coordinates
>
> Step 231826, time 463.652 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 191384000.000000, max 4098777344.000000 (between atoms 3033 and 3034)
> bonds that rotated more than 30 degrees:
> atom 1 atom 2  angle  previous, current, constraint length
>    1423   1424  140.4    0.1000 503.9983      0.1000
>    3024   3025   61.1    0.1236 223337872.0000      0.1090
>    3026   3027  168.8    6.6242 149263.5000      0.1090
>    3028   3029  165.8  5245.4102 263929.4375      0.1090
>    3031   3032  116.2    0.1090 223428336.0000      0.1090
>    3033   3034  179.9  426.5654 446766720.0000      0.1090
>    3035   3036   35.3   29.6105 831.0708      0.1090
>    3035   3037  102.9    0.7991 775.3371      0.1090
>    3038   3039   90.0    0.4497   0.6355      0.1090
>    3038   3040   47.7    0.2833   0.1111      0.1090
> step 231826: One or more water molecules can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
>
> So I checked the my input configuration. the 3035, 3028, 3035 atoms are
> ligand C atoms and the 3037, 3029, 3034 atoms are the ligand H atoms.
> Why does the LINCS warning      occurs? and How I solve this problem?
>
> Many Thanks
>
> Jinyoung
> --
> 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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