Re: [gmx-users] Removal of Waters in Hydrophobic Core
Thank you Chris,
I tried the commands and I was able to obtain an output
keep_these_waters.gro with about 3.5 MB of data. However, when I continued
with the rest of the commands:
tail -1 initial.gro > last_line.gro
head -$(expr $(cat initial.gro | wc -l | awk '{print $1}') - 1 )
initial.gro > not_last_line.gro
cat not_last_line.gro new_waters.gro last_line.gro > new_system.gro
editconf -f new_system.gro -o new_system_sequential_numbers.gro
I still failed to obtain a new structure. The structure is the same as
solvated.gro. I am going to put extreme z-coordinates to see if all the
water molecules will be removed. Other than that, do you have any
suggestions?
*Sanim Rahman*
B.S. Chemical Engineering, 2019
Undergraduate Researcher, Global Center for Hearing and Speech Research
On Fri, Nov 25, 2016 at 3:48 PM, Christopher Neale <
chris.ne...@alum.utoronto.ca> wrote:
> not sure if it is a typo or perhaps a command structure I am unfamiliar
> with, but I don't understand your command.
>
> Try this:
>
> chmod +x keepbyz.pl
> ./keepbyz.pl new_waters.gro > keep_these_waters.gro
>
> see here: http://www.gromacs.org/Documentation/How-tos/
> Membrane_Simulations?highlight=generates
>
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Sanim
> Rahman
> Sent: 24 November 2016 16:12:11
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] Removal of Waters in Hydrophobic Core
>
> Hello,
>
> I am currently working through the second tutorial of the Bevan Labs KALP15
> simulation. I am attempting to use the keepbyz.pl script to remove the
> waters in the hydrophobic core. I have designated a upperz and
> lowerz coordinated and followed the entire section highlighted in the
> instructions, however, my output (new_system_sequential_numbers.gro) has
> no
> deleted water molecules. It is the same system as solvated.gro.
>
> I believe my error is within the keepbyz.pl file, because when I input the
> command:
>
> chmod +x keepbyz.pl new_waters.gro > keep_these_waters.gro
>
> the file "keep_these_waters.gro" is an empty file.
>
> Here is my script for keepbyz.pl:
>
> #!/bin/bash
> # give new_waters.gro as first command line arguement
> upperz=5.821
> lowerz=0.574
> sol=SOL
> count=0
> cat $1 | grep "$sol" | while read line; do
> for first in $line; do
> break
> done
> if [ "$count" = 3 ]; then
> count=0
> fi
> count=$(expr $count + 1)
> if [ "$count" != 1 ]; then
> continue
> fi
> l=${#line}
> m=$(expr $l - 24) // would use -48 if velocities are also in .gro and
> -24 otherwise
> i=1
> for word in ${line:$m}; do
> if [ "$i" = 1 ]; then
> popex=$word
> else
> if [ "$i" = 2 ]; then
> popey=$word
> else
> if [ "$i" = 3 ]; then
> popez=$word
> break
> fi
> fi
> fi
> i=$(expr $i + 1)
> done
> nolx=`echo "$popez > $upperz" | bc`
> nohx=`echo "$popez < $lowerz" | bc`
> myno=$(expr $nolx + $nohx)
> if [ "$myno" != 0 ]; then
> z=${#first}
> if [ "$z" != 8 ]; then
> sfirst="[[:space:]]$first"
> else
> sfirst=$first
> fi
> `echo grep $sfirst $1`
> fi
> done
>
> I will appreciate the help!
>
> Regards,
>
> *Sanim Rahman*
> B.S. Chemical Engineering, 2019
> Resident Assistant, Castor Hall Engineering Living Learning Community
> 2016-2017
> Undergraduate Researcher, Global Center for Hearing and Speech Research
> Honors College Engineering Peer Advisor
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
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Re: [gmx-users] setting up a pull vec
You haven't told us what you want to do, but perhaps you want to pull them apart along the vector that connects the centers of mass of these two species. One possible way to do that is to use gmx traj -com to get the two centers of mass, then figure out the vector yourself. That's going to get messy if the whole complex tumbles in solution, so you could also add a few absolute position restraints to pin down one of the molecules. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of abhisek Mondal Sent: 25 November 2016 02:37:18 To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] setting up a pull vec Hi, I'm trying to run a umbrella sampling using following pull code: ; Pull code pull= yes pull_ngroups= 2 pull_ncoords= 1 pull_group1_name= JZ4 pull_group2_name= Protein_chain_A pull_coord1_type= umbrella ; harmonic biasing force pull_coord1_geometry= direction-periodic pull_coord1_groups = 1 2 pull_coord1_dim = Y Y Y ; pulling in all dimension pull_coord1_rate= 0.01 ; 0.01 nm per ps = 10 nm per ns pull_coord1_k = 500 ; kJ mol^-1 nm^-2 pull_coord1_start = yes ; define initial COM distance > 0 This approach needs me to specify a pulling vec which is essentially not 0,0,0. Could you please suggest me a way to decide how to provide the pull vec ? Thanks. -- Abhisek Mondal *Research Fellow* *Structural Biology and Bioinformatics Division* *CSIR-Indian Institute of Chemical Biology* *Kolkata 700032* *INDIA* -- 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] viscosity and surface tension
On 25/11/16 21:21, Andrew Bostick wrote: Dear gromacs users, How to calculate viscosity and surface tension in the simulation of some small molecules in the box of water. Best, Andrew Surface tension is done by extending the box with vacuum, at least twice the amount of volume, running a simulation and then extracting the number out the energy file. You may have problems equilibrating if the concentration is low. Viscosity, please check the pdf manual, there are some methods but it is not easy due to sampling. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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] Removal of Waters in Hydrophobic Core
not sure if it is a typo or perhaps a command structure I am unfamiliar with,
but I don't understand your command.
Try this:
chmod +x keepbyz.pl
./keepbyz.pl new_waters.gro > keep_these_waters.gro
see here:
http://www.gromacs.org/Documentation/How-tos/Membrane_Simulations?highlight=generates
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of Sanim Rahman
Sent: 24 November 2016 16:12:11
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Removal of Waters in Hydrophobic Core
Hello,
I am currently working through the second tutorial of the Bevan Labs KALP15
simulation. I am attempting to use the keepbyz.pl script to remove the
waters in the hydrophobic core. I have designated a upperz and
lowerz coordinated and followed the entire section highlighted in the
instructions, however, my output (new_system_sequential_numbers.gro) has no
deleted water molecules. It is the same system as solvated.gro.
I believe my error is within the keepbyz.pl file, because when I input the
command:
chmod +x keepbyz.pl new_waters.gro > keep_these_waters.gro
the file "keep_these_waters.gro" is an empty file.
Here is my script for keepbyz.pl:
#!/bin/bash
# give new_waters.gro as first command line arguement
upperz=5.821
lowerz=0.574
sol=SOL
count=0
cat $1 | grep "$sol" | while read line; do
for first in $line; do
break
done
if [ "$count" = 3 ]; then
count=0
fi
count=$(expr $count + 1)
if [ "$count" != 1 ]; then
continue
fi
l=${#line}
m=$(expr $l - 24) // would use -48 if velocities are also in .gro and
-24 otherwise
i=1
for word in ${line:$m}; do
if [ "$i" = 1 ]; then
popex=$word
else
if [ "$i" = 2 ]; then
popey=$word
else
if [ "$i" = 3 ]; then
popez=$word
break
fi
fi
fi
i=$(expr $i + 1)
done
nolx=`echo "$popez > $upperz" | bc`
nohx=`echo "$popez < $lowerz" | bc`
myno=$(expr $nolx + $nohx)
if [ "$myno" != 0 ]; then
z=${#first}
if [ "$z" != 8 ]; then
sfirst="[[:space:]]$first"
else
sfirst=$first
fi
`echo grep $sfirst $1`
fi
done
I will appreciate the help!
Regards,
*Sanim Rahman*
B.S. Chemical Engineering, 2019
Resident Assistant, Castor Hall Engineering Living Learning Community
2016-2017
Undergraduate Researcher, Global Center for Hearing and Speech Research
Honors College Engineering Peer Advisor
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[gmx-users] viscosity and surface tension
Dear gromacs users, How to calculate viscosity and surface tension in the simulation of some small molecules in the box of water. Best, Andrew -- 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] gmx distance -- gmx: double free or corruption
Please ignore the mention of this being an amber trajectory. I can reproduce the exact same behaviour by gmx distance -s my.pdb -f my.pdb , so the issue can be reproduced on the information in a PDB file alone (and that pdb looks just fine in VMD). Thank you, Chris. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Christopher Neale Sent: 25 November 2016 14:33:51 To: Discussion list for GROMACS users Subject: [gmx-users] gmx distance -- gmx: double free or corruption This sender failed our fraud detection checks and may not be who they appear to be. Learn about spoofing at http://aka.ms/LearnAboutSpoofing Dear Users: I am having trouble with gmx distance crashing in gromacs 5.1.2. I am trying to analyze the distance of different peptide residues from the center of a lipid bilayer. have CA atoms on residues 2-20 and also on residues 22-40 (2 peptides). If I try to do residues 2-20 it works fine. If I try to do residues 22 to 40, I get a memory error. Funny thing is, I narrowed it down to see that 22-36 is OK but 22-37 fails, then when I try 37 alone it is OK, and selections of 26-40 also work. Please note that all these tests were repeated 2x on an allocation with 128 GB of memory, so I don’t think I’m just describing a stochastic failure. I didn’t try newer versions of gromacs, but there is nothing in the release notes for any newer version that mentions “distance” or “select” that seems to be related to this. ## I run like this: inpstr=$(for((i=22;i<=40;i++)); do echo -n "com of (residue $i and name CA) plus com of (resname POPC or resname POPS) plus "; done|sed "s/plus $//") gmx distance -s gromacs.tpr -f gromacs.xtc -n index.ndx -select "$inpstr" -oxyz depthB.xvg I’ve also tried giving gmx distance a .pdb as input to the -s option, where I first ran gmx editconf -resnr 1 just to avoid any issues with possible double residue counting in the .tpr file, and the result is the same crash. I checked that the .pdb and the .xtc have the same number of atoms with gmx check and I also ran gmx select on these groups to ensure that an atom was picked up in all cases (it was). Also, VMD loading the .pdb extracted from the .tpr and the .xtc gives a sensible trajectory. As a final note, the simulation was actually run in amber. I then used a plugin-aware version go gmx trjconv to read in the amber netcdf trajectory file and output a gromacs .xtc file, which I used in a non-plugin-aware version of gromacs for the analyses. The .tpr was generated for the same system (actually, I generated the gromacs .tpr from a grompp -pp .top file that was used in amber tool parmed gromber to set up the amber run). ## The output (with error) is this: :-) GROMACS - gmx distance, VERSION 5.1.2 (-: GROMACS is written by: Emile Apol Rossen Apostolov Herman J.C. BerendsenPar Bjelkmar Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch Gerrit Groenhof Christoph Junghans Anca HamuraruVincent Hindriksen Dimitrios KarkoulisPeter KassonJiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff Erik Marklund Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers Peter TielemanTeemu 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 distance, VERSION 5.1.2 Executable: /oasis/scratch/comet/cneale/temp_project/exec/gromacs-5.1.2/exec_serial/bin/gmx Data prefix: /oasis/scratch/comet/cneale/temp_project/exec/gromacs-5.1.2/exec_serial Command line: gmx distance -s gromacs.tpr -f gromacs.xtc -n index.ndx -select 'com of (residue 22 and name CA) plus com of (resname POPC or resname POPS) plus com of (residue 23 and name CA) plus com of (resname POPC or resname POPS) plus com of (residue 24 and name CA) plus com of (resname POPC or resname POPS) plus com of (residue 25 and name CA) plus com of (resname POPC or resname POPS) plus com of (residue 26 and name CA) plus com of (resname POPC or resname POPS) plus com of (residue 27 and name CA) plus com of (resname POPC or resname POPS) plus com of (residue 28 and name CA) plus com of (resname POPC or resname POPS) p
[gmx-users] gmx distance -- gmx: double free or corruption
Dear Users: I am having trouble with gmx distance crashing in gromacs 5.1.2. I am trying to analyze the distance of different peptide residues from the center of a lipid bilayer. have CA atoms on residues 2-20 and also on residues 22-40 (2 peptides). If I try to do residues 2-20 it works fine. If I try to do residues 22 to 40, I get a memory error. Funny thing is, I narrowed it down to see that 22-36 is OK but 22-37 fails, then when I try 37 alone it is OK, and selections of 26-40 also work. Please note that all these tests were repeated 2x on an allocation with 128 GB of memory, so I don’t think I’m just describing a stochastic failure. I didn’t try newer versions of gromacs, but there is nothing in the release notes for any newer version that mentions “distance” or “select” that seems to be related to this. ## I run like this: inpstr=$(for((i=22;i<=40;i++)); do echo -n "com of (residue $i and name CA) plus com of (resname POPC or resname POPS) plus "; done|sed "s/plus $//") gmx distance -s gromacs.tpr -f gromacs.xtc -n index.ndx -select "$inpstr" -oxyz depthB.xvg I’ve also tried giving gmx distance a .pdb as input to the -s option, where I first ran gmx editconf -resnr 1 just to avoid any issues with possible double residue counting in the .tpr file, and the result is the same crash. I checked that the .pdb and the .xtc have the same number of atoms with gmx check and I also ran gmx select on these groups to ensure that an atom was picked up in all cases (it was). Also, VMD loading the .pdb extracted from the .tpr and the .xtc gives a sensible trajectory. As a final note, the simulation was actually run in amber. I then used a plugin-aware version go gmx trjconv to read in the amber netcdf trajectory file and output a gromacs .xtc file, which I used in a non-plugin-aware version of gromacs for the analyses. The .tpr was generated for the same system (actually, I generated the gromacs .tpr from a grompp -pp .top file that was used in amber tool parmed gromber to set up the amber run). ## The output (with error) is this: :-) GROMACS - gmx distance, VERSION 5.1.2 (-: GROMACS is written by: Emile Apol Rossen Apostolov Herman J.C. BerendsenPar Bjelkmar Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch Gerrit Groenhof Christoph Junghans Anca HamuraruVincent Hindriksen Dimitrios KarkoulisPeter KassonJiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff Erik Marklund Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers Peter TielemanTeemu 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 distance, VERSION 5.1.2 Executable: /oasis/scratch/comet/cneale/temp_project/exec/gromacs-5.1.2/exec_serial/bin/gmx Data prefix: /oasis/scratch/comet/cneale/temp_project/exec/gromacs-5.1.2/exec_serial Command line: gmx distance -s gromacs.tpr -f gromacs.xtc -n index.ndx -select 'com of (residue 22 and name CA) plus com of (resname POPC or resname POPS) plus com of (residue 23 and name CA) plus com of (resname POPC or resname POPS) plus com of (residue 24 and name CA) plus com of (resname POPC or resname POPS) plus com of (residue 25 and name CA) plus com of (resname POPC or resname POPS) plus com of (residue 26 and name CA) plus com of (resname POPC or resname POPS) plus com of (residue 27 and name CA) plus com of (resname POPC or resname POPS) plus com of (residue 28 and name CA) plus com of (resname POPC or resname POPS) plus com of (residue 29 and name CA) plus com of (resname POPC or resname POPS) plus com of (residue 30 and name CA) plus com of (resname POPC or resname POPS) plus com of (residue 31 and name CA) plus com of (resname POPC or resname POPS) plus com of (residue 32 and name CA) plus com of (resname POPC or resname POPS) plus com of (residue 33 and name CA) plus com of (resname POPC or resname POPS) plus com of (residue 34 and name CA) plus com of (resname POPC or resname POPS) plus com of (residue 35 and name CA) plus com of (resname POPC or resname POPS) plus com of (residue 36 and name CA) plus com of (resname POPC or resname POPS) plus com of (residue
[gmx-users] grp 1 does not have same number of elements as grp 1
Hello: I want to analyze order parameters for a 128 molecules of DPPC/ 128 moleculesDPPE/Drug membrane, but when i run gmx_order -s npt.tpr -f npt.xtc -n sn1.ndx -d z -od deuter_sn1.xvg, the following error appears: grp 1 does not have same number of elements as grp 1. I deleted 0-3 (System, DPPC, DPPE, Drug) and also 0-4 (System, DPPC, DPPE, Drug and TIP3)) and the error remains. What can i do in this case? Thanks -- 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.
