RE: [gmx-users] Exclusions in topology file seem not working for big systems
Hi, If you really had too many exclusions you would get an error message. So I just tested this. I used the couple_moltype option to couple a 389 atom protein. This generates exclusions between each protein atom and the 388 others. All interactions are excluded correctly (and re-added as special 1-4's because of the couple option). So I don't understand what is going wrong in your case. Berk Date: Wed, 2 Dec 2009 09:31:03 -0800 From: resa...@yahoo.com Subject: Re: [gmx-users] Exclusions in topology file seem not working for big systems To: gmx-users@gromacs.org Thanks for your response Dr van der Spoel. Then there is a limit on the number of atoms that can be defined in the exclusions section. My smaller system has 60 atoms and I used exclusions successfully for that, so I guess the limit might be a little more than 32. Regarding the use of energygrp_excl,it seems it does not work with PME. If I define the protein in the energygrp_excl group, grompp gives me this warning: Can not exclude the lattice Coulomb energy between energy groups Which I think means some of electrostatics is not going to be excluded between protein atoms. Is there a workaround for this? I think my last resort would be to run a simulation first with PME and without exclusions, and then rerunning it but this time by defining protein in the energygrp_excl and using cut-off instead of PME. Then I guess I will be left with only protein-water interactions. Regards, Reza Salari From: David van der Spoel To: Discussion list for GROMACS users Sent: Wed, December 2, 2009 11:59:49 AM Subject: Re: [gmx-users] Exclusions in topology file seem not working for big systems Reza Salari wrote: > Hi All, > > I seem to have a hard time to use exclusions in topology file. I have a > relatively big system (~400 aa) that I am trying to calculate the difference > in desolvation energy (dA) upon turning off charges on a specific residue > using thermodynamics integration method. The system is a complex of two > proteins and is frozen inside the box (for my project I need it to be > frozen).¨ You can have max 32 exclusions per atom AFAIK. However you can use energy_group_excluisions in the mdp file. > > To calculate the desolvation energy, I need to exclude all the non-bonding > interactions among protein atoms, then the dA that I get corresponds to the > desolvation energy (and doesn't include the lost interactions between mutated > residue and the rest of protein). I couldn't use energygrp_excl in mdp file > since I am using PME. So I defined exclusions in topology file as follows > (three-dot means that numbers continue to the last number): > > [ exclusions] > 1 2 3 4 5 6 ... 6420 > 2 1 3 4 5 6 ... 6420 > 3 1 2 4 5 6 ... 6420 > ... > ... > 6420 1 2 3 ... 6419 > > I used gmxdump to check that the exclusions were actually implemented, and it > seems that they were. > > However when I use g_energy, I don't get zero energy for short range > interactions. Here are the results of g_energy for simulations with and > without exclusions: > >Coul-SR:Protein-Protein LJ-SR:Protein-Protein > Coul-14:Protein-Protein LJ-14:Protein-Protein > no exclusions-20277.6 > -13030.737023.9 7890.52 > using exclusions-16221.2 > -10332.937023.9 > 7890.52 > > > I did the same test with a small system (~6 residue) and I did get zero SR > interactions. While the exclusions work for my small system, I don't know why > they seem not working for my bigger system. Am I missing something here or is > there something like an implicit limit for the number of atoms that can be > defined in the exclusion section of topology file? > > I appreciate any hint or help. > > Regards, > Reza Salari > -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone:46 18 471 4205fax: 46 18 511 755 sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php __
[gmx-users] "coarse_grain.tcl" script does not show all of the coarse-grained bonds in vmd
Hi all,
I was trying to show the bonds between my CG beads in VMD. I have four CG
beads per each molecule, and there are 18 separate molecules which contain
these four beads, which results in having 72 CG beads in total. Therefore,
I expect to see 54 CG bonds in the end.
I used the "coarse_grain.tcl" script to visualize these CG bonds as
suggested on the VMD page. I have two different bead types in the system: CA
and CG. In order to visualize the bonds I used the following command line on
Tk console:
source coarse_grained.tcl
g_cg -tpr topol.tpr -sel {{name "CA"} {name "CB"}} -rep {Licorice Licorice}
-color {name name}
After that it gave me the following lines:
[ g_cg ] Processing "topol.tpr"...
[ g_cg ] Create the bond list for 72 atoms...
[ g_cg ] Rebuild bonds...
[ g_cg ] Create representations...
which I understood that all the bonds are created successfully, but when I
looked at the screen I could see only one of those CG bonds, but not the
others. Why might be the reason?
Thanks in advance
--
Ozge Engin
★☆
--
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Re: [gmx-users] "coarse_grain.tcl" script does not show all of the coarse-grained bonds in vmd
Ozge Engin a écrit :
Hi all,
I was trying to show the bonds between my CG beads in VMD. I have four
CG beads per each molecule, and there are 18 separate molecules which
contain these four beads, which results in having 72 CG beads in
total. Therefore, I expect to see 54 CG bonds in the end.
I used the "coarse_grain.tcl" script to visualize these CG bonds as
suggested on the VMD page. I have two different bead types in the
system: CA and CG. In order to visualize the bonds I used the
following command line on Tk console:
source coarse_grained.tcl
g_cg -tpr topol.tpr -sel {{name "CA"} {name "CB"}} -rep {Licorice
Licorice} -color {name name}
Hi,
you mentionned that you have 2 types of beads called CA and CG. Here,
you are selecting beads named CA and CB. Maybe that's where the problem
come from. Try to modify the representations manually (from the
"representation" menu) to see if it change something. If not, that is
probably a bug in the parsing of the gmxdump output. That is where the
bonds come from.
Cheers,
Nicolas
After that it gave me the following lines:
[ g_cg ] Processing "topol.tpr"...
[ g_cg ] Create the bond list for 72 atoms...
[ g_cg ] Rebuild bonds...
[ g_cg ] Create representations...
which I understood that all the bonds are created successfully, but
when I looked at the screen I could see only one of those CG bonds,
but not the others. Why might be the reason?
Thanks in advance
--
Ozge Engin
★☆
<>--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
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[gmx-users] spatial distribution function (SDF)
Hai all... Did anyone know how to do spatial distribution functions??? I have 125 ion pairs in my system. The problem is, 1)how I can I get the 3-D probability distributions of anion around cation or cation around anion in my system? Could anybody tell me the method? 2)When I read the GROMACS manual, I should create 4 group in my index file. Can anybody tell me what is first, second, three and for group represent??? I already try to do it, but I'm failed to get the result.. Thanks IMA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: gmx-users Digest, Vol 68, Issue 21
etween energy groups > > Which I think means some of electrostatics is not going to be excluded > between protein atoms. Is there a workaround for this? I think my last > resort would be to run a simulation first with PME and without exclusions, > and then rerunning it but this time by defining protein in the > energygrp_excl and using cut-off instead of PME. Then I guess I will be > left with only protein-water interactions. > > Regards, > Reza Salari > > > From: David van der Spoel > To: Discussion list for GROMACS users > Sent: Wed, December 2, 2009 11:59:49 AM > Subject: Re: [gmx-users] Exclusions in topology file seem not working for > big systems > > > Reza Salari wrote: > > Hi All, > > > > I seem to have a hard time to use exclusions in topology file. I have a > relatively big system (~400 aa) that I am trying to calculate the difference > in desolvation energy (dA) upon turning off charges on a specific residue > using thermodynamics integration method. The system is a complex of two > proteins and is frozen inside the box (for my project I need it to be > frozen).¨ > > You can have max 32 exclusions per atom AFAIK. > However you can use energy_group_excluisions in the mdp file. > > > > To calculate the desolvation energy, I need to exclude all the > non-bonding interactions among protein atoms, then the dA that I get > corresponds to the desolvation energy (and doesn't include the lost > interactions between mutated residue and the rest of protein). I couldn't > use energygrp_excl in mdp file since I am using PME. So I defined > exclusions in topology file as follows (three-dot means > that numbers continue to the last number): > > > > [ exclusions] > > 1 2 3 4 5 6 ... 6420 > > 2 1 3 4 5 6 ... 6420 > > 3 1 2 4 5 6 ... 6420 > > ... > > ... > > 6420 1 2 3 ... 6419 > > > > I used gmxdump to check that the exclusions were actually implemented, > and it seems that they were. > > > > However when I use g_energy, I don't get zero energy for short range > interactions. Here are the results of g_energy for simulations with and > without exclusions: > > > >Coul-SR:Protein-Protein LJ-SR:Protein-Protein > Coul-14:Protein-Protein LJ-14:Protein-Protein > > no exclusions-20277.6 > -13030.737023.9 > 7890.52 > > using exclusions-16221.2 >-10332.9 > 37023.9 >7890.52 > > > > > > I did the same test with a small system (~6 residue) and I did get zero > SR interactions. While the exclusions work for my small system, I don't know > why they seem not working for my bigger system. Am I missing something here > or is there something like an implicit limit for the number of atoms that > can be defined in the exclusion section of topology file? > > > > I appreciate any hint or help. > > > > Regards, > > Reza Salari > > > > > -- David. > > David van der Spoel, PhD, Professor of Biology > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: 46 18 471 4205fax: 46 18 511 > 755 > sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se > > -- gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > _ > New Windows 7: Find the right PC for you. Learn more. > http://windows.microsoft.com/shop > -- next part -- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20091203/31581af5/attachment-0001.html > > -- > > Message: 3 > Date: Thu, 3 Dec 2009 11:23:46 +0200 > From: Ozge Engin > Subject: [gmx-users] "coarse_grain.tcl" script does not show all of >the coarse-grained bonds in vmd > To: gmx-users@gromacs.org > Message-ID: ><373874cf0912030123q30e9dd86ve61c8845eec46...@mail.gmail.com> > Content-Type: text/plain; charset=&q
[gmx-users] Protonation and solvation software
What is the best software for protonating and for solvating pdb files for doing Molecular Dynamics with GROMACS?. Best regards. Lucio. Lucio Ricardo Montero Valenzuela Instituto de Biotecnologia, UNAM Departamento de Biologia Molecular de Plantas Av. Universidad 2001, Col. Chamilpa Cuernavaca 62210 Mexico Este mensaje fue enviado desde el servidor Webmail del Instituto de Biotecnologia. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: amber force field in Gromacs
Dear Servaas,
Tested again in 'vacuum' and I saw no problems. Here goes what I did:
#--
cat << EOF >| leap.in
verbosity 1
source leaprc.ff99SB
ad = sequence { DA5 DA DA3 }
saveamberparm ad da_amber.top da_amber.crd
savepdb ad DA.pdb
quit
EOF
tleap -f leap.in >| leap.out
acpypi -x da_amber.crd -p da_amber.top -d # acpypi generates em.mdp and
md.mdp
cat << EOF >| md.mdp
cpp = /usr/bin/cpp
define = ;-DFLEXIBLE
integrator = md
nsteps = 25
constraints = none
emtol= 1000.0
emstep = 0.01
comm_mode= angular
ns_type = simple
nstlist = 0
rlist= 0
rcoulomb = 0
rvdw = 0
Tcoupl = no
Pcoupl = no
gen_vel = no
nstxout = 100
pbc = no
EOF
editconf -bt cubic -d 1.0 -f da_amber_GMX.gro -o da_amber_GMX.gro
#Single precision
grompp -f em.mdp -c da_amber_GMX.gro -p da_amber_GMX.top -o em.tpr
mdrun -v -deffnm em
grompp -f md.mdp -c em.gro -p da_amber_GMX.top -o md.tpr
mdrun -v -deffnm md
vmd md.gro md.trr
#--
As you may suspect from the beginning it may be something in your mdp file.
Case the example above works, I would suggest you to try the mdp for solvent
box I sent before in a long simulation.
Good luck.
Regards,
Alan
On Wed, Dec 2, 2009 at 11:10, Alan wrote:
> Dear Servaas,
>
> In tleap did you really did:
>
> TLEAP
> tleap -f leaprc.ff99SB
> ad = sequence { DA5 DA DA3 }
> saveamberparm da da_amber.top da_amber.crd
>
>
> If so, it's wrong, it should be:
>
> saveamberparm ad da_amber.top da_amber.crd
>^^^
> and not 'da'
>
> Besides, I tried to reproduce what you did using what I think would be
> fine and... everything went fine! Energies after minimisation in
> single and double were almost identical and trajectories diverted
> normally.
>
> Please check what I did.
>
> # begin commands
>
> cat << EOF >| em.mdp
> define = -DFLEXIBLE
> integrator = cg ; steep
> nsteps = 200
> constraints = none
> emtol= 1000.0
> nstcgsteep = 10 ; do a steep every 10 steps of cg
> emstep = 0.01 ; used with steep
> nstcomm = 1
> coulombtype = PME
> ns_type = grid
> rlist= 1.0
> rcoulomb = 1.0
> rvdw = 1.4
> Tcoupl = no
> Pcoupl = no
> gen_vel = no
> nstxout = 0 ; write coords every # step
> optimize_fft = yes
> EOF
>
>
> cat << EOF >| md.mdp
> integrator = md
> nsteps = 1000
> dt = 0.002
> constraints = all-bonds
> nstcomm = 1
> ns_type = grid
> rlist= 1.2
> rcoulomb = 1.1
> rvdw = 1.0
> vdwtype = shift
> rvdw-switch = 0.9
> coulombtype = PME-Switch
> Tcoupl = v-rescale
> tau_t= 0.1 0.1
> tc-grps = protein non-protein
> ref_t= 300 300
> Pcoupl = parrinello-rahman
> Pcoupltype = isotropic
> tau_p= 0.5
> compressibility = 4.5e-5
> ref_p= 1.0
> gen_vel = yes
> nstxout = 2 ; write coords every # step
> lincs-iter = 2
> DispCorr = EnerPres
> optimize_fft = yes
> EOF
>
>
> cat << EOF >| leap.in
> verbosity 1
> source leaprc.ff99SB
> ad = sequence { DA5 DA DA3 }
> solvatebox ad TIP3PBOX 10.0
> addions ad Na+ 5
> addions ad Cl- 3
> saveamberparm ad da_amber.top da_amber.crd
> savepdb ad DA.pdb
> quit
> EOF
> tleap -f leap.in >| leap.out
>
> acpypi -x da_amber.crd -p da_amber.top -d
>
> #Single precision
> grompp -f em.mdp -c da_amber_GMX.gro -p da_amber_GMX.top -o em.tpr
> mdrun -v -deffnm em
>
> #Polak-Ribiere Conjugate Gradients converged to Fmax < 1000 in 22 steps
> #Potential Energy = -6.2280516e+04
> #Maximum force = 7.5868494e+02 on atom 98
> #Norm of force = 1.0447179e+02
>
> grompp -f md.mdp -c em.gro -p da_amber_GMX.top -o md.tpr
> mdrun -v -deffnm md
>
> #Double precision
> grompp_d -f em.mdp -c da_amber_GMX.gro -p da_amber_GMX.top -o em.tpr
> mdrun_d -v -deffnm em
>
> #Polak-Ribiere Conjugate Gradients converged to Fmax < 1000 in 22 steps
> #Potential Energy = -6.22813514022256e+04
> #Maximum force = 7.58238100790309e+02 on atom 98
> #Norm of force = 1.04358667410458e+02
>
> grompp_d -f md.mdp -c em.gro -p da_amber_GMX.top -o md.tpr
> mdrun_d -v -deffnm md
>
> # end commands
>
> Reg
[gmx-users] Fatal error: No such moleculetype Na
Hi All, I am trying to run the tutorial " http://code.google.com/p/acpypi/wiki/TutorialAcpypi4Gromacs"; for using ACPYPI generated topology with GROMACS. I am using amber99sb forcefield for one docked complex. It is running successfully upto genion and giving error while doing grompp for energy minimization -- --- Program grompp_d, VERSION 4.0.5 Source code file: toppush.c, line: 1641 Fatal error: No such moleculetype Na --- I tried adding ions entries from amber99sb.rtp to ions.itp and ended up with same error. I tried instruction given at " http://www.mail-archive.com/gmx-users@gromacs.org/msg20965.html"; which also resulted in same error. I was able to successfully perform EM as well as MD without adding ions i.e bypassing the genion step. Please, suggest me the way to get rid of this error. With thanks, Vivek -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Fatal error: No such moleculetype Na
vivek sharma wrote: Hi All, I am trying to run the tutorial "http://code.google.com/p/acpypi/wiki/TutorialAcpypi4Gromacs"; for using ACPYPI generated topology with GROMACS. I am using amber99sb forcefield for one docked complex. It is running successfully upto genion and giving error while doing grompp for energy minimization -- --- Program grompp_d, VERSION 4.0.5 Source code file: toppush.c, line: 1641 Fatal error: No such moleculetype Na --- I tried adding ions entries from amber99sb.rtp to ions.itp and ended up with same error. I tried instruction given at "http://www.mail-archive.com/gmx-users@gromacs.org/msg20965.html"; which also resulted in same error. I was able to successfully perform EM as well as MD without adding ions i.e bypassing the genion step. Please, suggest me the way to get rid of this error. Can you post the relevant entry in ions.itp? If you followed the instructions at the link you posted correctly, then you shouldn't have this problem. Maybe someone can spot the mistake. -Justin With thanks, Vivek -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re:gmx-users Digest, Vol 67, Issue 150 (memory allocationerror)
hema dhevi wrote: hai justin, ya its robust. and urs is the only tutorial which i found for transmembrane protein MD simulation in GROMACS. Its really useful. thank you. As you said i tried it in other system also there i used gromacs version 3.3.3. i am getting the same kind of error. I didnt use any special configuration flags for installation, for both the versions and in both the systems. And the compiler which i am using is gcc version 4.1.2 20070626 (Red Hat 4.1.2-14) The gcc-4.1.x series are broken, and have long been known to be the cause of several problems reported to this list. Please upgrade your compiler to a more modern one (I believe all newer versions of gcc work fine, per my own usage), and re-install Gromacs. -Justin Thanks in advance with regards N.Hema Dhevi -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Protonation and solvation software
Lucio Ricardo Montero Valenzuela wrote: What is the best software for protonating and for solvating pdb files for doing Molecular Dynamics with GROMACS?. The Gromacs tools themselves - pdb2gmx allows you to select protonation states and add back any necessary hydrogen atoms when generating the topology, and genbox does solvation. -Justin Best regards. Lucio. Lucio Ricardo Montero Valenzuela Instituto de Biotecnologia, UNAM Departamento de Biologia Molecular de Plantas Av. Universidad 2001, Col. Chamilpa Cuernavaca 62210 Mexico Este mensaje fue enviado desde el servidor Webmail del Instituto de Biotecnologia. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Reducing Standard Error output
Our first run typically produces this output Getting Loaded... Reading file md.tpr, VERSION 4.0.5 (single precision) Loaded with Money starting mdrun 'Protein in water' 500 steps, 1.0 ps. step 0 step 100, remaining runtime:95 s Fraction complete: 0.2 step 200, remaining runtime:70 s Fraction complete: 0.4 step 300, remaining runtime:46 s Fraction complete: 0.6 step 400, remaining runtime:23 s Fraction complete: 0.8 Writing final coordinates. step 500, remaining runtime: 0 s Fraction complete: 1 Parallel run - timing based on wallclock. NODE (s) Real (s) (%) Time:119.000119.000100.0 1:59 (Mnbf/s) (GFlops) (ns/day) (hour/ns) Performance: 55.372 3.138 0.728 32.990 gcq#0: Thanx for Using GROMACS - Have a Nice Day For our project's workflow we are extending the simulations using these arguments, -v -x -c -o -e -cpo next.cpt -cpi md.cpt -deffnm md but I notice there is much more standard error output than I was expecting, in addition to a LINCS WARNING. Should I be worried about that warning? Is there a way we can turn off these error reports for each timestep? Step 785, time 1.57 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.051275, max 3.234419 (between atoms 2396 and 2397) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2396 2397 103.70.0973 0.4065 0.0960 Step 786, time 1.572 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.31, max 0.001926 (between atoms 2396 and 2397) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2396 2397 69.50.4065 0.0962 0.0960 -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_densmap and xpm files
Hi all. I have a question about xpm files produced by g_densmap. I would like, if possible, to extract information in numerical format, such as for example a single txt file with three columns 'x y density' for all the points on the grid chosen. These should be the information which are contained inside the xpm file but I cannot understand how to extract them. Any suggestion? Thank you for your help, Alb -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] PBC screw
Hello, grompp 4.0.5 gave me the following error message. ERROR: invalid enum 'full' for variable pbc, using 'xyz' Next time use one of: 'xyz' 'no' 'xy' 'screw' Could someone tell me what does the "screw" option? I cant find it into paper and online manual, as well as at the gmx-list. bests eef ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 +55.11.4437-0196 http://fileti.ufabc.edu.br -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
R: [gmx-users] g_densmap and xpm files
In my previous e-mail I was not clear enough... extracting x and y values from xpm is easy and it is also easy to extract the density informations since they are represented by letters and for each of them a corresponding value of the number density is given at the beginning of the file. In my file I have 2000 values for the x and 2000 for the y and I got correctly 400 values for the density . However I don't understand how they are organized in the file. The first 2000 lines should be associated to the first value of the x and varying values of the y (2000 values) or is it the opposite or something else? Thank you Alb Messaggio originale Da: albita...@virgilio.it Data: 3-dic-2009 12.44 PM A: Ogg: [gmx-users] g_densmap and xpm files Hi all. I have a question about xpm files produced by g_densmap. I would like, if possible, to extract information in numerical format, such as for example a single txt file with three columns 'x y density' for all the points on the grid chosen. These should be the information which are contained inside the xpm file but I cannot understand how to extract them. Any suggestion? Thank you for your help, Alb -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] spatial distribution function (SDF)
g_spatial -h -or- g_sdf -h -- original message -- ai all... Did anyone know how to do spatial distribution functions??? I have 125 ion pairs in my system. The problem is, 1)how I can I get the 3-D probability distributions of anion around cation or cation around anion in my system? Could anybody tell me the method? 2)When I read the GROMACS manual, I should create 4 group in my index file. Can anybody tell me what is first, second, three and for group represent??? I already try to do it, but I'm failed to get the result.. Thanks IMA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Heat of vaporization in gromacs
Hi, Please let me know which of the gromacs utilities is responsible for heat of vaporization calculation. Thanks in advance, Vitaly -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Heat of vaporization in gromacs
Vitaly V. Chaban wrote: Hi, Please let me know which of the gromacs utilities is responsible for heat of vaporization calculation. Thanks in advance, Vitaly g_energy and you. you need liquid and gas phase simulations. -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Reducing Standard Error output
Hi Jack, The option -v is for verbose output. The LINCS warnings may indicate an issue regarding the stability of your system. They usually precede crashes. Maybe you need to equilibrate a bit further. Hope it helps, Tsjerk On Thu, Dec 3, 2009 at 1:26 PM, Jack Shultz wrote: > Our first run typically produces this output > > Getting Loaded... > Reading file md.tpr, VERSION 4.0.5 (single precision) > Loaded with Money > > starting mdrun 'Protein in water' > 500 steps, 1.0 ps. > > step 0 > step 100, remaining runtime: 95 s Fraction complete: 0.2 > > step 200, remaining runtime: 70 s Fraction complete: 0.4 > > step 300, remaining runtime: 46 s Fraction complete: 0.6 > > step 400, remaining runtime: 23 s Fraction complete: 0.8 > > Writing final coordinates. > > step 500, remaining runtime: 0 s Fraction complete: 1 > > Parallel run - timing based on wallclock. > > NODE (s) Real (s) (%) > Time: 119.000 119.000 100.0 > 1:59 > (Mnbf/s) (GFlops) (ns/day) (hour/ns) > Performance: 55.372 3.138 0.728 32.990 > > gcq#0: Thanx for Using GROMACS - Have a Nice Day > > > For our project's workflow we are extending the simulations using > these arguments, > -v -x -c -o -e -cpo next.cpt -cpi md.cpt -deffnm md > > but I notice there is much more standard error output than I was > expecting, in addition to a LINCS WARNING. Should I be worried about > that warning? > Is there a way we can turn off these error reports for each timestep? > > Step 785, time 1.57 (ps) LINCS WARNING > relative constraint deviation after LINCS: > rms 0.051275, max 3.234419 (between atoms 2396 and 2397) > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint length > 2396 2397 103.7 0.0973 0.4065 0.0960 > > Step 786, time 1.572 (ps) LINCS WARNING > relative constraint deviation after LINCS: > rms 0.31, max 0.001926 (between atoms 2396 and 2397) > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint length > 2396 2397 69.5 0.4065 0.0962 0.0960 > > > -- > Jack > > http://drugdiscoveryathome.com > http://hydrogenathome.org > -- > gmx-users mailing list gmx-us...@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Reducing Standard Error output
Thanks, I just figured out removing the -v will reduce output. Interestingly I only have this problem with 64-bit Windows hosts. I have not observed it in any others and I have a fairly diverse environment on this project. For now I can say removing the -v gets the app to finish the run. Jack On Thu, Dec 3, 2009 at 10:36 AM, Tsjerk Wassenaar wrote: > Hi Jack, > > The option -v is for verbose output. > The LINCS warnings may indicate an issue regarding the stability of > your system. They usually precede crashes. Maybe you need to > equilibrate a bit further. > > Hope it helps, > > Tsjerk > > On Thu, Dec 3, 2009 at 1:26 PM, Jack Shultz > wrote: >> Our first run typically produces this output >> >> Getting Loaded... >> Reading file md.tpr, VERSION 4.0.5 (single precision) >> Loaded with Money >> >> starting mdrun 'Protein in water' >> 500 steps, 1.0 ps. >> >> step 0 >> step 100, remaining runtime: 95 s Fraction complete: 0.2 >> >> step 200, remaining runtime: 70 s Fraction complete: 0.4 >> >> step 300, remaining runtime: 46 s Fraction complete: 0.6 >> >> step 400, remaining runtime: 23 s Fraction complete: 0.8 >> >> Writing final coordinates. >> >> step 500, remaining runtime: 0 s Fraction complete: 1 >> >> Parallel run - timing based on wallclock. >> >> NODE (s) Real (s) (%) >> Time: 119.000 119.000 100.0 >> 1:59 >> (Mnbf/s) (GFlops) (ns/day) (hour/ns) >> Performance: 55.372 3.138 0.728 32.990 >> >> gcq#0: Thanx for Using GROMACS - Have a Nice Day >> >> >> For our project's workflow we are extending the simulations using >> these arguments, >> -v -x -c -o -e -cpo next.cpt -cpi md.cpt -deffnm md >> >> but I notice there is much more standard error output than I was >> expecting, in addition to a LINCS WARNING. Should I be worried about >> that warning? >> Is there a way we can turn off these error reports for each timestep? >> >> Step 785, time 1.57 (ps) LINCS WARNING >> relative constraint deviation after LINCS: >> rms 0.051275, max 3.234419 (between atoms 2396 and 2397) >> bonds that rotated more than 30 degrees: >> atom 1 atom 2 angle previous, current, constraint length >> 2396 2397 103.7 0.0973 0.4065 0.0960 >> >> Step 786, time 1.572 (ps) LINCS WARNING >> relative constraint deviation after LINCS: >> rms 0.31, max 0.001926 (between atoms 2396 and 2397) >> bonds that rotated more than 30 degrees: >> atom 1 atom 2 angle previous, current, constraint length >> 2396 2397 69.5 0.4065 0.0962 0.0960 >> >> >> -- >> Jack >> >> http://drugdiscoveryathome.com >> http://hydrogenathome.org >> -- >> gmx-users mailing list gmx-us...@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > > > -- > Tsjerk A. Wassenaar, Ph.D. > > Computational Chemist > Medicinal Chemist > Neuropharmacologist > -- > gmx-users mailing list gmx-us...@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] What is the exact difference in the g_energy output between LJ(1-4) LJ(SR) and LJ(LR)?
Hi, As per the title. I need to understand what is the difference to help myself debug my inane efforts at CG parametrization. LJ(1-4) I think is clear (non bonded, non-coulombic interactions between 1-4 pairs described in the topology), but about the rest? thanks! m. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Exclusions in topology file seem not working for big systems
Thanks Dr Hess. I didn't get an error message when using grompp, then I think I didn't have too many exclusions. I didn't know about using couple_type in this context before. If I get it correctly, if I want to exclude all non-bonding interactions inside a protein using couple_type, I must define it as follows in each mdp file for each lambda: (I need to decouple all the non-bonding intra molecular interactions for each lambdas): couple_moltype=protein couple_lambda0=none couple_lambda1=none couple-intramol=none If this is right, I will test it for my system which has ~7000 protein atoms. BTW I am still a little confused about the reported 1-4 energies while using exclusions, could you please explain this?. For my smaller system I got zero SR but non-zero 1-4 energies, even that the interactions between all the atoms were excluded. If I remove the pairs in topology file I would get no 1-4 term along with a different dV/dl value. So does it mean if I want to exclude all the intramolecular interactions I have to remove pairs? (my system is frozen and therefore I am not worried about the conformational change of the protein and also I am mainly interested in dV/dl values, which in this case is related to the electrostatic interaction of a residue with water as the charges on that residue being turned off). Regards, Reza Salari From: Berk Hess To: Discussion list for GROMACS users Sent: Thu, December 3, 2009 3:30:27 AM Subject: RE: [gmx-users] Exclusions in topology file seem not working for big systems Hi, If you really had too many exclusions you would get an error message. So I just tested this. I used the couple_moltype option to couple a 389 atom protein. This generates exclusions between each protein atom and the 388 others. All interactions are excluded correctly (and re-added as special 1-4's because of the couple option). So I don't understand what is going wrong in your case. Berk Date: Wed, 2 Dec 2009 09:31:03 -0800 From: resa...@yahoo.com Subject: Re: [gmx-users] Exclusions in topology file seem not working for big systems To: gmx-users@gromacs.org Thanks for your response Dr van der Spoel. Then there is a limit on the number of atoms that can be defined in the exclusions section. My smaller system has 60 atoms and I used exclusions successfully for that, so I guess the limit might be a little more than 32. Regarding the use of energygrp_excl,it seems it does not work with PME. If I define the protein in the energygrp_excl group, grompp gives me this warning: Can not exclude the lattice Coulomb energy between energy groups Which I think means some of electrostatics is not going to be excluded between protein atoms. Is there a workaround for this? I think my last resort would be to run a simulation first with PME and without exclusions, and then rerunning it but this time by defining protein in the energygrp_excl and using cut-off instead of PME. Then I guess I will be left with only protein-water interactions. Regards, Reza Salari From: David van der Spoel To: Discussion list for GROMACS users Sent: Wed, December 2, 2009 11:59:49 AM Subject: Re: [gmx-users] Exclusions in topology file seem not working for big systems Reza Salari wrote: > Hi All, > > I seem to have a hard time to use exclusions in topology file. I have a > relatively big system (~400 aa) that I am trying to calculate the difference > in desolvation energy (dA) upon turning off charges on a specific residue > using thermodynamics integration method. The system is a complex of two > proteins and is frozen inside the box (for my project I need it to be > frozen).¨ You can have max 32 exclusions per atom AFAIK. However you can use energy_group_excluisions in the mdp file. > > To calculate the desolvation energy, I need to exclude all the non-bonding > interactions among protein atoms, then the dA that I get corresponds to the > desolvation energy (and doesn't include the lost interactions between mutated > residue and the rest of protein). I couldn't use energygrp_excl in mdp file > since I am using PME. So I defined exclusions in topology file as follows > (three-dot means that numbers continue to the last number): > > [ exclusions] > 1 2 3 4 5 6 ... 6420 > 2 1 3 4 5 6 ... 6420 > 3 1 2 4 5 6 ... 6420 > ... > ... > 6420 1 2 3 ... 6419 > > I used gmxdump to check that the exclusions were actually implemented, and it > seems that they were. > > However when I use g_energy, I don't get zero energy for short range > interactions. Here are the results of g_energy for simulations with and > without exclusions: > >Coul-SR:Protein-Protein LJ-SR:Protein-Protein > Coul-14:Protein-Protein LJ-14:Protein-Protein > no exclusions-20277.6 >-13030.7
RE: [gmx-users] Exclusions in topology file seem not working for big systems
Hi, I think that for your problem the couple option is not useful. It does exactly the opposite. I removes all interactions of the selected molecule type with the rest of the system and transform all interactions within the molecule by "vacuum" non-cutoff LJ and Coulomb interactions. (which end up in special 1-4 energy terms). Berk Date: Thu, 3 Dec 2009 08:59:12 -0800 From: resa...@yahoo.com Subject: Re: [gmx-users] Exclusions in topology file seem not working for big systems To: gmx-users@gromacs.org Thanks Dr Hess. I didn't get an error message when using grompp, then I think I didn't have too many exclusions. I didn't know about using couple_type in this context before. If I get it correctly, if I want to exclude all non-bonding interactions inside a protein using couple_type, I must define it as follows in each mdp file for each lambda: (I need to decouple all the non-bonding intra molecular interactions for each lambdas): couple_moltype=protein couple_lambda0=none couple_lambda1=none couple-intramol=none If this is right, I will test it for my system which has ~7000 protein atoms. BTW I am still a little confused about the reported 1-4 energies while using exclusions, could you please explain this?. For my smaller system I got zero SR but non-zero 1-4 energies, even that the interactions between all the atoms were excluded. If I remove the pairs in topology file I would get no 1-4 term along with a different dV/dl value. So does it mean if I want to exclude all the intramolecular interactions I have to remove pairs? (my system is frozen and therefore I am not worried about the conformational change of the protein and also I am mainly interested in dV/dl values, which in this case is related to the electrostatic interaction of a residue with water as the charges on that residue being turned off). Regards, Reza Salari From: Berk Hess To: Discussion list for GROMACS users Sent: Thu, December 3, 2009 3:30:27 AM Subject: RE: [gmx-users] Exclusions in topology file seem not working for big systems Hi, If you really had too many exclusions you would get an error message. So I just tested this. I used the couple_moltype option to couple a 389 atom protein. This generates exclusions between each protein atom and the 388 others. All interactions are excluded correctly (and re-added as special 1-4's because of the couple option). So I don't understand what is going wrong in your case. Berk Date: Wed, 2 Dec 2009 09:31:03 -0800 From: resa...@yahoo.com Subject: Re: [gmx-users] Exclusions in topology file seem not working for big systems To: gmx-users@gromacs.org Thanks for your response Dr van der Spoel. Then there is a limit on the number of atoms that can be defined in the exclusions section. My smaller system has 60 atoms and I used exclusions successfully for that, so I guess the limit might be a little more than 32. Regarding the use of energygrp_excl,it seems it does not work with PME. If I define the protein in the energygrp_excl group, grompp gives me this warning: Can not exclude the lattice Coulomb energy between energy groups Which I think means some of electrostatics is not going to be excluded between protein atoms. Is there a workaround for this? I think my last resort would be to run a simulation first with PME and without exclusions, and then rerunning it but this time by defining protein in the energygrp_excl and using cut-off instead of PME. Then I guess I will be left with only protein-water interactions. Regards, Reza Salari From: David van der Spoel To: Discussion list for GROMACS users Sent: Wed, December 2, 2009 11:59:49 AM Subject: Re: [gmx-users] Exclusions in topology file seem not working for big systems Reza Salari wrote: > Hi All, > > I seem to have a hard time to use exclusions in topology file. I have a > relatively big system (~400 aa) that I am trying to calculate the difference > in desolvation energy (dA) upon turning off charges on a specific residue > using thermodynamics integration method. The system is a complex of two > proteins and is frozen inside the box (for my project I need it to be > frozen).¨ You can have max 32 exclusions per atom AFAIK. However you can use energy_group_excluisions in the mdp file. > > To calculate the desolvation energy, I need to exclude all the non-bonding > interactions among protein atoms, then the dA that I get corresponds to the > desolvation energy (and doesn't include the lost interactions between mutated > residue and the rest of protein). I couldn't use energygrp_excl in mdp file > since I am using PME. So I defined exclusions in topology file as follows > (three-dot means that numbers continue to the last number): > > [ exclusions] > 1 2 3 4 5 6 ... 6420 > 2 1 3 4 5 6 ... 6420 > 3 1 2 4 5 6 ... 6420 > ... > ... > 6420 1 2 3 ... 6419 > > I used gmxdump to check that the exclusions were actually implemented, and it > seems that they were. >
[gmx-users] LIE method
Dear users, I want to estimate the affinity of a protein to two diferent ligands and compare the results. Is the LIE the best method to do that? Does any one have a reference that this kind of analysis is performed or an example of mdp? Best regards, Tatiana -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Exclusions in topology file seem not working for big systems
Thank you very much Dr Hess. Then I guess I have to test my rerun workaround that I mentioned for my system. About 1-4 interactions in general, could you a little bit about 1-4 energies while using exclusions please? I hope I am not missing something obvious. The main thing that I am not sure about is if I want to exclude all non-bonding interactions inside a small molecule, do I need to remove [pairs] when adding the [exclusions]? I am using OPLSAA. Regards, Reza Salari From: Berk Hess To: Discussion list for GROMACS users Sent: Thu, December 3, 2009 12:06:53 PM Subject: RE: [gmx-users] Exclusions in topology file seem not working for big systems Hi, I think that for your problem the couple option is not useful. It does exactly the opposite. I removes all interactions of the selected molecule type with the rest of the system and transform all interactions within the molecule by "vacuum" non-cutoff LJ and Coulomb interactions. (which end up in special 1-4 energy terms). Berk Date: Thu, 3 Dec 2009 08:59:12 -0800 From: resa...@yahoo.com Subject: Re: [gmx-users] Exclusions in topology file seem not working for big systems To: gmx-users@gromacs.org Thanks Dr Hess. I didn't get an error message when using grompp, then I think I didn't have too many exclusions. I didn't know about using couple_type in this context before. If I get it correctly, if I want to exclude all non-bonding interactions inside a protein using couple_type, I must define it as follows in each mdp file for each lambda: (I need to decouple all the non-bonding intra molecular interactions for each lambdas): couple_moltype=protein couple_lambda0=none couple_lambda1=none couple-intramol=none If this is right, I will test it for my system which has ~7000 protein atoms. BTW I am still a little confused about the reported 1-4 energies while using exclusions, could you please explain this?. For my smaller system I got zero SR but non-zero 1-4 energies, even that the interactions between all the atoms were excluded. If I remove the pairs in topology file I would get no 1-4 term along with a different dV/dl value. So does it mean if I want to exclude all the intramolecular interactions I have to remove pairs? (my system is frozen and therefore I am not worried about the conformational change of the protein and also I am mainly interested in dV/dl values, which in this case is related to the electrostatic interaction of a residue with water as the charges on that residue being turned off). Regards, Reza Salari From: Berk Hess To: Discussion list for GROMACS users Sent: Thu, December 3, 2009 3:30:27 AM Subject: RE: [gmx-users] Exclusions in topology file seem not working for big systems Hi, If you really had too many exclusions you would get an error message. So I just tested this. I used the couple_moltype option to couple a 389 atom protein. This generates exclusions between each protein atom and the 388 others. All interactions are excluded correctly (and re-added as special 1-4's because of the couple option). So I don't understand what is going wrong in your case. Berk Date: Wed, 2 Dec 2009 09:31:03 -0800 From: resa...@yahoo.com Subject: Re: [gmx-users] Exclusions in topology file seem not working for big systems To: gmx-users@gromacs.org Thanks for your response Dr van der Spoel. Then there is a limit on the number of atoms that can be defined in the exclusions section. My smaller system has 60 atoms and I used exclusions successfully for that, so I guess the limit might be a little more than 32. Regarding the use of energygrp_excl,it seems it does not work with PME. If I define the protein in the energygrp_excl group, grompp gives me this warning: Can not exclude the lattice Coulomb energy between energy groups Which I think means some of electrostatics is not going to be excluded between protein atoms. Is there a workaround for this? I think my last resort would be to run a simulation first with PME and without exclusions, and then rerunning it but this time by defining protein in the energygrp_excl and using cut-off instead of PME. Then I guess I will be left with only protein-water interactions. Regards, Reza Salari From: David van der Spoel To: Discussion list for GROMACS users Sent: Wed, December 2, 2009 11:59:49 AM Subject: Re: [gmx-users] Exclusions in topology file seem not working for big systems Reza Salari wrote: > Hi All, > > I seem to have a hard time to use exclusions in topology file. I have a > relatively big system (~400 aa) that I am trying to calculate the difference > in desolvation energy (dA) upon turning off charges on a specific residue > using thermodynamics integration method. The system is a complex of two > proteins and is frozen inside the box (for my project I
[gmx-users] topology and rtp file
Hello Gmx Usrs, I am new to Gromacs. I am trying to simulate a protein-membrane complex using berger-oplsaa combination . I have created a topology file for the protein using pdb2gmx in order to then build up the topology for my system using the include file mechanism. After that I tried to use my system.top in grompp ( grompp -f xx.mdp -c system.pdb -p system.top -o out.tpr ) but I get a warning about atoms in top and pdb does not match. I went trough the mailing list but I have still doubt. I checked where were the differences. It seems that the order of the aromatic ring in the pdb and in the top didn't match. To be clear (tyr as example but the same problem occur with his): .pdb .top N N HN H CA CA HA HA CB CB HB1 HB1 HB2 HB2 CG CG CD1 CD1 HD1 HD1 CE1 CD2 HE1 HD2 CZ CE1 OH HE1 HH CE2 CD2 HE2 HD2 CZ CE2 OH HE2 HH C C O O Is this because the .top seems follow the order presents in the rtp file that I have (am I right?). Assuming that this is the case I am wondering if changing the atoms order in the rtp from: [ TYR ] [ atoms ] N opls_238 -0.500 1 H opls_241 0.300 1 CA opls_224B 0.140 1 HA opls_140 0.060 1 CB opls_149 -0.005 2 HB1 opls_140 0.060 2 HB2 opls_140 0.060 2 CG opls_145 -0.115 3 CD1 opls_145 -0.115 4 HD1 opls_146 0.115 4 CD2 opls_145 -0.115 5 HD2 opls_146 0.115 5 CE1 opls_145 -0.115 6 HE1 opls_146 0.115 6 CE2 opls_145 -0.115 7 HE2 opls_146 0.115 7 CZ opls_166 0.150 8 OH opls_167 -0.585 8 HH opls_168 0.435 8 C opls_235 0.500 9 O opls_236 -0.500 9 to: [ TYR ] [ atoms ] N opls_238 -0.500 1 H opls_241 0.300 1 CA opls_224B 0.140 1 HA opls_140 0.060 1 CB opls_149 -0.005 2 HB1 opls_140 0.060 2 HB2 opls_140 0.060 2 CG opls_145 -0.115 3 CD1 opls_145 -0.115 4 HD1 opls_146 0.115 4 CE1 opls_145 -0.115 6 HE1 opls_146 0.115 6 CZ opls_166 0.150 8 OH opls_167 -0.585 8 HH opls_168 0.435 8 CE2 opls_145 -0.115 7 HE2 opls_146 0.115 7 CD2 opls_145 -0.115 5 HD2 opls_146 0.115 5 C opls_235 0.500 9 O opls_236 -0.500 9 can that have a further effect since it seems that the file handling is based on line position and not atoms name. Any suggestions are welcome Thanks Irene -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] topology and rtp file
irene farabella wrote: Hello Gmx Usrs, I am new to Gromacs. I am trying to simulate a protein-membrane complex using berger-oplsaa combination . I have created a topology Have you properly modified the Berger parameters for use with OPLS-AA? Otherwise, the results you will get will be nonsense :) file for the protein using pdb2gmx in order to then build up the topology for my system using the include file mechanism. After that I tried to use my system.top in grompp ( grompp -f xx.mdp -c system.pdb -p system.top -o out.tpr ) but I get a warning about atoms in top and pdb does not match. I went trough the mailing list Is system.pdb the cleaned up output from pdb2gmx? It is also better to post the actual error message. The topology and coordinate file may not match in terms of atom names or in terms of the number of coordinates, which are both very different problems. I guess you are referring to a naming mismatch? but I have still doubt. I checked where were the differences. It seems that the order of the aromatic ring in the pdb and in the top didn't match. To be clear (tyr as example but the same problem occur with his): .pdb .top N N HNH If this is what's in your .pdb file, then you aren't using the pdb2gmx output, are you? CA CA HA HA CB CB HB1 HB1 HB2 HB2 CG CG CD1 CD1 HD1 HD1 CE1 CD2 HE1 HD2 CZ CE1 OH HE1 HH CE2 CD2 HE2 HD2 CZ CE2 OH HE2 HH CC O O Is this because the .top seems follow the order presents in the rtp file that I have (am I right?). Yes, pdb2gmx will output according to the .rtp entry. Assuming that this is the case I am wondering if changing the atoms order in the rtp from: [ TYR ] [ atoms ] Nopls_238 -0.500 1 Hopls_2410.300 1 CAopls_224B 0.140 1 HAopls_1400.060 1 CBopls_149 -0.005 2 HB1opls_1400.060 2 HB2opls_1400.060 2 CGopls_145 -0.115 3 CD1opls_145 -0.115 4 HD1opls_1460.115 4 CD2opls_145 -0.115 5 HD2opls_1460.115 5 CE1opls_145 -0.115 6 HE1opls_1460.115 6 CE2opls_145 -0.115 7 HE2opls_1460.115 7 CZopls_1660.150 8 OHopls_167 -0.585 8 HHopls_1680.435 8 Copls_2350.500 9 Oopls_236 -0.500 9 to: [ TYR ] [ atoms ] Nopls_238 -0.500 1 Hopls_2410.300 1 CAopls_224B 0.140 1 HAopls_1400.060 1 CBopls_149 -0.005 2 HB1opls_1400.060 2 HB2opls_1400.060 2 CGopls_145 -0.115 3 CD1opls_145 -0.115 4 HD1opls_1460.115 4 CE1opls_145 -0.115 6 HE1opls_1460.115 6 CZopls_1660.150 8 OHopls_167 -0.585 8 HHopls_1680.435 8 CE2opls_145 -0.115 7 HE2opls_1460.115 7 CD2opls_145 -0.115 5 HD2opls_1460.115 5 Copls_2350.500 9 Oopls_236 -0.500 9 can that have a further effect since it seems that the file handling is based on line position and not atoms name. If you re-arrange the .rtp file, you'll have to start all over again, since only pdb2gmx uses the .rtp files. I doubt this is meaningful. If you've got a .pdb file with HN as the amide proton, then it won't match the topology, which specifies this atom as H. There will still be a name mismatch, but not an order mismatch, which simply indicates to me that you are using the wrong coordinate file. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] helix tilt
How can I calculate the angle between a helix inserted in a membrane and the axis perpendicular to the surface of the membrane. I have tried using g_helixorient, but the graphs all come as a straight line in zero. Thank you -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] 1-4 interaction energies in g_energy
Hi, Please suggest why is the reason that 1-4 term is not displayed (to be selected for calculation) in the g_energy utility? I have two kinds of objects (with 25 and 5 atoms) in my system - with "nexcl" equal to 3 and 2. I guess the 1-4 term may not be displayed if there is no 1-4 interactions but in this system they are evidently present. What the problem can be here? Thanks, Vitaly -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] PBC screw
Hi, please someone correct me if I'm wrong, but the equivalent of Gromacs 3.3.x : pbc = full is pbc = xyz periodic_molecules = yes since Gromacs 4.0. Oliver http://manual.gromacs.org/current/online/mdp_opt.html#nl On Thu, Dec 3, 2009 at 08:22, Eudes Fileti wrote: > Hello, > grompp 4.0.5 gave me the following error message. > ERROR: invalid enum 'full' for variable pbc, using 'xyz' > Next time use one of: 'xyz' 'no' 'xy' 'screw' > Could someone tell me what does the "screw" option? > I cant find it into paper and online manual, as well as at the gmx-list. > bests > eef -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] looking for polar lipid pdb
Grateful for receiving DOPC.pdb file thanks francesco pietra -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] looking for polar lipid pdb
http://persweb.wabash.edu/facstaff/fellers/ -Justin Francesco Pietra wrote: Grateful for receiving DOPC.pdb file thanks francesco pietra -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Pressure annealing in Gromacs?
Jussi Lehtola wrote: On Thu, 2009-12-03 at 02:30 +1100, Mark Abraham wrote: Jussi Lehtola wrote: I'm experiencing trouble converging the density of some heavy liquid alcohols (after 10 ns of simulation the density is still changing linearly). Is there any way to run pressure annealing in Gromacs? Running the system through a high pressure and temperature might give an equilibrium structure quicker. There's nothing native that I'm aware of, but it should be straightforward to use sed or perl in a script to do the annealing "by hand" in a series of mdrun invocations. Yup, that came to mind but then one ends up with N trajectories and log files. And one has to run a big pile of grompp commands, that waste some parallel run time, so I really would like something integrated. One of the hidden beauties of checkpoint files might be that you can prepare all the .tpr off-line, and just match them up while running, and use mdrun -append to concatenate files. I'd give that idea a solid test before using on something I cared about though! If it worked, the only inferiority would be repetitious parallel setup. Besides, a thing like changing the reference pressure should be a no-brainer in the source code - assuming the code is well structured and one knows it well beforehand. Agreed. For all I know, there are some state variables in the above checkpoint solution that shouldn't be carried over when the reference pressure changes, anyway. Anyway, the problem was solved for now already. Still, pressure annealing would be a nice addon to gromacs. (I'll open a bug on bugzilla about it.) Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] helix tilt
Stefan Hoorman wrote: How can I calculate the angle between a helix inserted in a membrane and the axis perpendicular to the surface of the membrane. I have tried using g_helixorient, but the graphs all come as a straight line in zero. See -z in g_sgangle -h Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] What is the exact difference in the g_energy output between LJ(1-4) LJ(SR) and LJ(LR)?
ms wrote: Hi, As per the title. I need to understand what is the difference to help myself debug my inane efforts at CG parametrization. LJ(1-4) I think is clear (non bonded, non-coulombic interactions between 1-4 pairs described in the topology), but about the rest? See manual 4.6.3 Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Reducing Standard Error output
Jack Shultz wrote: Thanks, I just figured out removing the -v will reduce output. Interestingly I only have this problem with 64-bit Windows hosts. I have not observed it in any others and I have a fairly diverse environment on this project. For now I can say removing the -v gets the app to finish the run. mdrun -v will have no effect on correct completion, unless the use of -v is causing some I/O buffer external to GROMACS to over-run. I suspect your observation indicates you were comparing apples and oranges. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] 1-4 interaction energies in g_energy
Vitaly V. Chaban wrote: Hi, Please suggest why is the reason that 1-4 term is not displayed (to be selected for calculation) in the g_energy utility? I have two kinds of objects (with 25 and 5 atoms) in my system - with "nexcl" equal to 3 and 2. I guess the 1-4 term may not be displayed if there is no 1-4 interactions but in this system they are evidently present. What the problem can be here? Hard to say - we can't see your topologies or even know what your objects are. You may have some manual exclusions or some such. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Fatal error: No such moleculetype Na
vivek sharma wrote: Hi All, I am trying to run the tutorial "http://code.google.com/p/acpypi/wiki/TutorialAcpypi4Gromacs"; for using ACPYPI generated topology with GROMACS. I am using amber99sb forcefield for one docked complex. It is running successfully upto genion and giving error while doing grompp for energy minimization -- --- Program grompp_d, VERSION 4.0.5 Source code file: toppush.c, line: 1641 Fatal error: No such moleculetype Na --- I tried adding ions entries from amber99sb.rtp to ions.itp and ended up with same error. I tried instruction given at "http://www.mail-archive.com/gmx-users@gromacs.org/msg20965.html"; which also resulted in same error. I was able to successfully perform EM as well as MD without adding ions i.e bypassing the genion step. Please, suggest me the way to get rid of this error. Probably by correctly installing the information about ions. See the website from which you got the AMBER port. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] spatial distribution function (SDF)
First three groups are the reference group, from which the SDF is generated, it sets the coordinate system. That means you need to have at least three "atoms" in the "molecule" you are generating the SDF from. Catch ya, Dr Dallas Warren Pharmacy and Pharmaceutical Sciences Monash University A polar bear is a Cartesian bear that has undergone a polar transformation -Original Message- From: gmx-users-boun...@gromacs.org on behalf of naimah haron naimah Sent: Thu 12/3/2009 9:03 PM To: gromacs Subject: [gmx-users] spatial distribution function (SDF) Hai all... Did anyone know how to do spatial distribution functions??? I have 125 ion pairs in my system. The problem is, 1)how I can I get the 3-D probability distributions of anion around cation or cation around anion in my system? Could anybody tell me the method? 2)When I read the GROMACS manual, I should create 4 group in my index file. Can anybody tell me what is first, second, three and for group represent??? I already try to do it, but I'm failed to get the result.. Thanks IMA <>-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] What is the exact difference in the g_energy output between LJ(1-4) LJ(SR) and LJ(LR)?
Mark Abraham ha scritto: > ms wrote: >> Hi, >> >> As per the title. I need to understand what is the difference to help >> myself debug my inane efforts at CG parametrization. LJ(1-4) I think is >> clear (non bonded, non-coulombic interactions between 1-4 pairs >> described in the topology), but about the rest? > > See manual 4.6.3 Seen it, still don't get it :) m. > Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Reducing Standard Error output
yes the environment I was running in was the boinc wrapper and its supposed to somehow return the standard error output. It probably got overloaded. It is curious why I only had the problem on windows 64 but I'm not going to worry about it. On Thu, Dec 3, 2009 at 6:33 PM, Mark Abraham wrote: > Jack Shultz wrote: >> >> Thanks, >> >> I just figured out removing the -v will reduce output. Interestingly I >> only have this problem with 64-bit Windows hosts. I have not observed >> it in any others and I have a fairly diverse environment on this >> project. For now I can say removing the -v gets the app to finish the >> run. > > mdrun -v will have no effect on correct completion, unless the use of -v is > causing some I/O buffer external to GROMACS to over-run. I suspect your > observation indicates you were comparing apples and oranges. > > Mark > -- > gmx-users mailing list gmx-us...@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] What is the exact difference in the g_energy output between LJ(1-4) LJ(SR) and LJ(LR)?
ms wrote: Mark Abraham ha scritto: ms wrote: Hi, As per the title. I need to understand what is the difference to help myself debug my inane efforts at CG parametrization. LJ(1-4) I think is clear (non bonded, non-coulombic interactions between 1-4 pairs described in the topology), but about the rest? See manual 4.6.3 Seen it, still don't get it :) A good reason to search the mailing list... http://lists.gromacs.org/pipermail/gmx-users/2007-December/031264.html -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Radial distribution specifications
Dear all, I need to plot the radial distribution functions but I am not sure how you specified the different radial pair distribution functions for H2O: gOO, gOH and gHH, in order to have different plots. Please, can you help me out with this? Thank you, Lum -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Radial distribution specifications
Lum Nforbi wrote: Dear all, I need to plot the radial distribution functions but I am not sure how you specified the different radial pair distribution functions for H2O: gOO, gOH and gHH, in order to have different plots. Please, can you help me out with this? Use index groups that contain the atoms of interest. -Justin Thank you, Lum -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: 1-4 interaction energies in g_energy
>> Hi, >> >> Please suggest why is the reason that 1-4 term is not displayed (to be >> selected for calculation) in the g_energy utility? I have two kinds of >> objects (with 25 and 5 atoms) in my system - with "nexcl" equal to 3 >> and 2. I guess the 1-4 term may not be displayed if there is no 1-4 >> interactions but in this system they are evidently present. >> >> What the problem can be here? > > Hard to say - we can't see your topologies or even know what your > objects are. You may have some manual exclusions or some such. > What do you mean saying "manual exclusions"? I have no energy exclusions defined in grompp.mdp. Is there any place to make them? Vitaly -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
