[gmx-users] Interatomic distance matrices
Dear Gromacs users, I was wondering, is there any utility in Gromacs for calculating and saving a triangular matrix of interatomic distances from a trajectory frame? The website mailing list search seems to be down, and Google has not been of much help. g_rmsdist looks like it *might* be able to do this, but from the documentation I can't tell whether or not there is a set of switches that would allow one to turn off the averaging/rms calculation features and instead generate a single frame static distance matrix. If Gromacs can't do this, can anyone recommend another program that could generate such matrices? This would not be hard to code, but time savers are always appreciated. :) Best Wishes, Nathan -- J. Nathan Scott, Ph.D. Postdoctoral Fellow Department of Chemistry and Biochemistry Montana State University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Replacing a residue and continuing a simulation run
Hello all, I was wondering, is it possible to replace a residue and then continue a simulation using the new parameters/geometry of the new residue? The reason I ask is that I am interested in performing simulations of proteins with tryptophan in its excited state following a lengthy equilibration with TRP in its ground state. I already have reliable excited state atomic charges for the TRP atoms, and I suppose that I will need to change at least some bonded terms to account for the altered geometry of the excited state. I am still in the middle of reading the information that is out there regarding parameterizing new molecules (since I'm using the CHARMM FF, I've been starting to follow Alexander MacKerell's protocols), but I'm still not quite sure as to how one would practically do this residue replacement in the context of a Gromacs run. Will I need to manually edit my .top file, or is there perhaps another way to update the topology file with the new residue following the ground state equilibration? How about coordinates, will I need to transform the TRP coordinates to the excited state geometry by hand? Perhaps the most important question: is there a better way to do the sort of residue replacement I'm contemplating, or is this something that is just inherently going to be a bit messy? Thanks very much for any insight or guidance you can offer! -- -- J. Nathan Scott, Ph.D. Postdoctoral Fellow Department of Chemistry and Biochemistry Montana State University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Trouble loading User data with a Tcl script (only half the data seems to load)
Hello all,
I have written a script that does per-time-step coloring of the water
molecules, residues, and ions in my protein based on electric field values I
previously calculated. I received excellent help here a few months sorting
out some problems with the script, but there is one big one remaining that I
hope someone can help with.
The problem is that only half the frames (the first half) in my simulation
are getting colored, and I can't figure out why. This happens no matter how
many frames I load, whether the full trajectory or just a few hundred
frames. For what it's worth, the machine I'm running on has 12 GB of RAM, a
very nice video card, and a new Xeon quad core processor, so I don't think
this is an issue of system resources. At least I can see that there is still
tons of free RAM when I am experiencing this issue.
Also, I would sincerely appreciate any advice on speeding up one of my
loops. To color the water molecules and ions I can simply atomselect them
all, and then loop through the values from the electric field data file for
that timestep and assign the color value to a user list either 3 or 1 times
respectively to color each atom.
However, for the residues in the protein I am having to atomselect them one
at a time, get the number of atoms for that residue, and then do another
loop to build a list of the correct length to assign the user values to each
atom of the residue. Can anyone recommend a more efficient way of coloring
the residues? When the residue coloring part of the script is stripped out
it runs so much faster despite the fact that there are far fewer protein
atoms than there are water or ion atoms, so I know this method of assignment
is sluggish.
Please see the script below my signature, and thank you in advance for any
advice you can provide.
--
--
J. Nathan Scott, Ph.D.
Postdoctoral Fellow
Department of Chemistry and Biochemistry
Montana State University
###
set first 0;
set last 1000;
set mut wt;
set mut_ wt_;
set i $first; #i will be timestep/filename indicator,
set j 0;
mol new /data/1stn/xtc/1stn_$mut.gro type gro waitfor all
mol addfile /data/1stn/xtc/1stn_$mut.xtc type xtc waitfor all first $first
last $l$
set mol_ID top;
set n [ molinfo $mol_ID get numframes ];
animate goto 0
animate delete beg 0 end 0 skip 0 0
mol delrep 0 $mol_ID
while {$i <= $last} {
set fp [open "/data/1stn/$mut/pd5/pd5.stripped/1stn_$mut_$i.pd5" r]
set file_data [read $fp]
close $fp
set data [split $file_data "\n"]
foreach {one} $data {
lappend efield [lindex $one 3]
}
### Looping through residues in the for loop,
### selecting one residue at a time, getting its number of atoms,
### and then building a user value list for each of those
### atoms in another for loop.
for {set k 6} {$k <= 141} {incr k} {
set prot [atomselect $mol_ID "resid $k" frame $j]
set num [$prot num]
$prot frame $j
set user_list {}
set u [lindex $efield [expr $k - 6]]
for {set b 1} {$b <= $num} {incr b} {
lappend user_list $u
}
$prot set user $user_list
$prot delete
}
### Water loop works well
set wat [atomselect $mol_ID waters frame $j]
$wat frame $j
set user_list {}
for {set a 136} {$a < 10233} {incr a} {
set u [lindex $efield $a]
lappend user_list $u $u $u
}
$wat set user $user_list
$wat delete
### Ion loop works well too
set ions [atomselect $mol_ID ions frame $j]
$ions frame $j
set user_list {}
for {set a 10233} {$a < 10243} {incr a} {
set u [lindex $efield $a]
lappend user_list $u
}
$ions set user $user_list
$ions delete
unset efield
incr j 1
incr i 2
}
--
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[gmx-users] Re: Trouble loading User data with a Tcl script (only half the data seems to load)
Hello again, fellow gmx-users,
I finally found my coding error that only set the User data for the first
half of the frames loaded, it was a simple indexing error after all.
However, I would still *greatly* appreciate any assistance with speeding up
the following loop:
for {set k 6} {$k <= 141} {incr k} {
set prot [atomselect $mol_ID "resid $k" frame $j]
set num [$prot num]
$prot frame $j
set user_list {}
set u [lindex $efield [expr $k - 6]]
for {set b 1} {$b <= $num} {incr b} {
lappend user_list $u
}
$prot set user $user_list
$prot delete
}
Is there a simpler way to accomplish the task of assigning a single User
value to individual residues without first atomselecting each one, getting
its number of atoms, and then finally looping over the atoms to build a
user_list? I'm hoping that there is some better way to do this that I
haven't thought of yet. My script runs very wonderfully except for this
chunk.
Thanks in advance for any help you can provide,
-Nathan
On Wed, May 4, 2011 at 11:06 AM, J. Nathan Scott <
scot...@chemistry.montana.edu> wrote:
> Hello all,
>
> I have written a script that does per-time-step coloring of the water
> molecules, residues, and ions in my protein based on electric field values I
> previously calculated. I received excellent help here a few months sorting
> out some problems with the script, but there is one big one remaining that I
> hope someone can help with.
>
> The problem is that only half the frames (the first half) in my simulation
> are getting colored, and I can't figure out why. This happens no matter how
> many frames I load, whether the full trajectory or just a few hundred
> frames. For what it's worth, the machine I'm running on has 12 GB of RAM, a
> very nice video card, and a new Xeon quad core processor, so I don't think
> this is an issue of system resources. At least I can see that there is still
> tons of free RAM when I am experiencing this issue.
>
> Also, I would sincerely appreciate any advice on speeding up one of my
> loops. To color the water molecules and ions I can simply atomselect them
> all, and then loop through the values from the electric field data file for
> that timestep and assign the color value to a user list either 3 or 1 times
> respectively to color each atom.
>
> However, for the residues in the protein I am having to atomselect them one
> at a time, get the number of atoms for that residue, and then do another
> loop to build a list of the correct length to assign the user values to each
> atom of the residue. Can anyone recommend a more efficient way of coloring
> the residues? When the residue coloring part of the script is stripped out
> it runs so much faster despite the fact that there are far fewer protein
> atoms than there are water or ion atoms, so I know this method of assignment
> is sluggish.
>
> Please see the script below my signature, and thank you in advance for any
> advice you can provide.
>
> --
> --
> J. Nathan Scott, Ph.D.
> Postdoctoral Fellow
> Department of Chemistry and Biochemistry
> Montana State University
>
>
>
>
> ###
> set first 0;
> set last 1000;
> set mut wt;
> set mut_ wt_;
> set i $first; #i will be timestep/filename indicator,
> set j 0;
>
> mol new /data/1stn/xtc/1stn_$mut.gro type gro waitfor all
> mol addfile /data/1stn/xtc/1stn_$mut.xtc type xtc waitfor all first $first
> last $l$
> set mol_ID top;
> set n [ molinfo $mol_ID get numframes ];
> animate goto 0
> animate delete beg 0 end 0 skip 0 0
> mol delrep 0 $mol_ID
>
> while {$i <= $last} {
> set fp [open "/data/1stn/$mut/pd5/pd5.stripped/1stn_$mut_$i.pd5" r]
> set file_data [read $fp]
> close $fp
>
> set data [split $file_data "\n"]
> foreach {one} $data {
> lappend efield [lindex $one 3]
> }
>
> ### Looping through residues in the for loop,
> ### selecting one residue at a time, getting its number of atoms,
> ### and then building a user value list for each of those
> ### atoms in another for loop.
>
> for {set k 6} {$k <= 141} {incr k} {
> set prot [atomselect $mol_ID "resid $k" frame $j]
> set num [$prot num]
> $prot frame $j
> set user_list {}
> set u [lindex $efield [expr $k - 6]]
> for {set b 1} {$b <= $num} {incr b} {
>lappend user_list $u
> }
> $prot set user $user_list
> $prot delete
> }
>
> ### Water loop works well
>
&g
[gmx-users] Re: Trouble loading User data with a Tcl script (only half the data seems to load)
Oops, this message and the original should have gone to the VMD mailing list
and not Gromacs of course. My mistake, apologies for cluttering your inbox.
:-)
-Nathan
On Thu, May 5, 2011 at 3:35 PM, J. Nathan Scott <
scot...@chemistry.montana.edu> wrote:
> Hello again, fellow gmx-users,
>
> I finally found my coding error that only set the User data for the first
> half of the frames loaded, it was a simple indexing error after all.
> However, I would still *greatly* appreciate any assistance with speeding up
> the following loop:
>
>
> for {set k 6} {$k <= 141} {incr k} {
> set prot [atomselect $mol_ID "resid $k" frame $j]
> set num [$prot num]
> $prot frame $j
> set user_list {}
> set u [lindex $efield [expr $k - 6]]
> for {set b 1} {$b <= $num} {incr b} {
>lappend user_list $u
> }
> $prot set user $user_list
> $prot delete
> }
>
> Is there a simpler way to accomplish the task of assigning a single User
> value to individual residues without first atomselecting each one, getting
> its number of atoms, and then finally looping over the atoms to build a
> user_list? I'm hoping that there is some better way to do this that I
> haven't thought of yet. My script runs very wonderfully except for this
> chunk.
>
> Thanks in advance for any help you can provide,
>
> -Nathan
>
>
> On Wed, May 4, 2011 at 11:06 AM, J. Nathan Scott <
> scot...@chemistry.montana.edu> wrote:
>
>> Hello all,
>>
>> I have written a script that does per-time-step coloring of the water
>> molecules, residues, and ions in my protein based on electric field values I
>> previously calculated. I received excellent help here a few months sorting
>> out some problems with the script, but there is one big one remaining that I
>> hope someone can help with.
>>
>> The problem is that only half the frames (the first half) in my simulation
>> are getting colored, and I can't figure out why. This happens no matter how
>> many frames I load, whether the full trajectory or just a few hundred
>> frames. For what it's worth, the machine I'm running on has 12 GB of RAM, a
>> very nice video card, and a new Xeon quad core processor, so I don't think
>> this is an issue of system resources. At least I can see that there is still
>> tons of free RAM when I am experiencing this issue.
>>
>> Also, I would sincerely appreciate any advice on speeding up one of my
>> loops. To color the water molecules and ions I can simply atomselect them
>> all, and then loop through the values from the electric field data file for
>> that timestep and assign the color value to a user list either 3 or 1 times
>> respectively to color each atom.
>>
>> However, for the residues in the protein I am having to atomselect them
>> one at a time, get the number of atoms for that residue, and then do another
>> loop to build a list of the correct length to assign the user values to each
>> atom of the residue. Can anyone recommend a more efficient way of coloring
>> the residues? When the residue coloring part of the script is stripped out
>> it runs so much faster despite the fact that there are far fewer protein
>> atoms than there are water or ion atoms, so I know this method of assignment
>> is sluggish.
>>
>> Please see the script below my signature, and thank you in advance for any
>> advice you can provide.
>>
>> --
>> --
>> J. Nathan Scott, Ph.D.
>> Postdoctoral Fellow
>> Department of Chemistry and Biochemistry
>> Montana State University
>>
>>
>>
>>
>> ###
>> set first 0;
>> set last 1000;
>> set mut wt;
>> set mut_ wt_;
>> set i $first; #i will be timestep/filename indicator,
>> set j 0;
>>
>> mol new /data/1stn/xtc/1stn_$mut.gro type gro waitfor all
>> mol addfile /data/1stn/xtc/1stn_$mut.xtc type xtc waitfor all first $first
>> last $l$
>> set mol_ID top;
>> set n [ molinfo $mol_ID get numframes ];
>> animate goto 0
>> animate delete beg 0 end 0 skip 0 0
>> mol delrep 0 $mol_ID
>>
>> while {$i <= $last} {
>> set fp [open "/data/1stn/$mut/pd5/pd5.stripped/1stn_$mut_$i.pd5"
>> r]
>> set file_data [read $fp]
>> close $fp
>>
>> set data [split $file_data "\n"]
>> foreach {one} $data {
>> lappend efield [lindex $one 3]
>> }
>
[gmx-users] Question regarding freeze groups and their use
Hi all, I know there has been a *lot* of discussion on the mailing list on using freezegrps and potential pitfalls, but after having read much of this discussion the past couple of days and the manual I still find myself with questions and problems I'm hoping someone can help with. What I want to do, specifically, is have my protein frozen (*not* just constrained with some large force, I need actual freezing of every protein atom) but have the solvent still react to the frozen protein. The purpose behind this is to compare the water behavior near a particular part of a protein when it is dynamic and when it is not and thereby learn something about the "communication" between protein and solvent in this case. However, it seems that I'm not finding a rational set of mdp options to allow this, at least not a set for which dynamics will run with any speed. I have tried many of the things people have discussed on the mailing list, including turning off constraints, turning off pressure coupling, reducing the Protein heat bath temperature to 0 K, and using energygrp_excl. Here are the parameters I just tried: integrator = md nsteps = 100 dt = 0.001 nstxout = 1 nstvout = 1 nstxtcout = 1 nstenergy = 1 nstlog = 1 continuation= yes constraints = none ns_type = grid nstlist = 5 rlist = 1.0 rcoulomb= 1.0 rvdw= 1.0 coulombtype = PME pme_order = 4 fourierspacing = 0.16 tcoupl = V-rescale tc-grps = Protein Non-Protein tau_t = 0.1 0.1 ref_t = 0 300 pcoupl = no pbc = xyz DispCorr= EnerPres gen_vel = no freezegrps = Protein freezedim = Y Y Y ;;; This ran, but *incredibly* slowly (I'm using a single 32 processor node, and only got 255 steps in 10 wallclock minutes). From the discussions I've read on the mailing list it seems that PME is somewhat less than ideal for simulations involving frozen atoms, but I used PME for electrostatics in my non-frozen simulations and would like to keep that consistent if possible (I do get a grompp warning of course). I am also getting warnings in the log file like: "DD step 254 vol min/aver 0.183! load imb.: force 2395.3% pme mesh/force 1.243" which I believe must be due to the frozen protein causing difficulties with domain decomposition. Can anyone offer any advice regarding these issues? I know this has been discussed often, but nothing I'm finding in the archives is particularly relevant. -- -- J. Nathan Scott, Ph.D. Postdoctoral Fellow Department of Chemistry and Biochemistry Montana State University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Question on checkpoint files and restarts/continuity
Hi all,
I had a very quick question I couldn't find an exact answer for that
I'm sure someone here can answer very easily. The Gromacs website says
(http://www.gromacs.org/Documentation/File_Formats/Checkpoint_File):
"A .cpt file is produced by mdrun at specified intervals (mdrun -cpt),
and contains information on all the state variables in a simulated
system. In the case of a crash (hardware failure, power outage, etc),
a checkpoint file can be used to resume the simulation exactly as it
was before the failure. Simulations can also be extended using a
checkpoint file.
During the course of a normal mdrun process (provided that it runs for
longer than one -cpt interval), two checkpoint files will be written,
state.cpt and state_prev.cpt. When extending simulations, use
state.cpt; the state_prev.cpt is a backup copy of the previous
checkpoint, maintained in case something goes wrong at the current
checkpoint. To convince yourself of this fact, you can inspect the
contents of a checkpoint file with gmxcheck."
My question is, does the checkpoint file have to contain positions,
velocities, *and* forces to preserve continuity? If forces are *not*
included in the checkpoint file, would that mean that they'd be
recalculated based on positions when the simulation resumes, thereby
creating a (slight) discontinuity in the trajectory?
On a closely related topic, some colleagues are attempting to use an
existing trajectory to start new simulations ("branching" points if
you will). I have advised them that using grompp's -time option, the
.trr file, and the .edr file for the existing trajectory to generate
new .tpr files is probably the way to go, since positions and
velocities will be read from the .trr file (their .trr file does not
contain any force information) and the information from the .edr file
will preserve system equilibration via the coupling constants. They
actually *want* these simulations to diverge. Have I misunderstood
anything about the way these files are used/work? Does this seem like
a reasonable procedure or is there a preferred method for doing
something like this?
Thanks in advance for any help you can provide.
--
--
J. Nathan Scott, Ph.D.
Postdoctoral Fellow
Department of Chemistry and Biochemistry
Montana State University
--
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[gmx-users] Question about adding hydrogens to a newly constructed residue
Hello fellow GROMACS users, I am in the process of constructing a new residue in the OPLS-AA force field for the mCherry chromophore. However, I am having some difficulty in adding three CH3 hydrogens. In the 2H5Q PDB structure the chromophore residue, CH6, has CE1 and CE2 ring carbons defined, but also an extended chain carbon named CE. The problem is that my hdb rules were assigning HE1 and HE2 to the ring carbon hydrogens (1 1 HE1 CE1 CD1 CZ for example), and HE1, HE2, and HE3 to the CE carbon hydrogens (3 4 HE CE SD CG1). Since these hydrogens are of different types, I need to have them named distinctly in my RTP file and need for Gromacs to understand them as different types. I changed the CH6 residue's CE atom to CE3 in the PDB file and the relevant RTP entries accordingly (see below). I also changed the hdb entry for the new CE3 atom (also below). Relevant RTP lines: CE3opls_209 0.0 10 HE31opls_140 0.0 11 HE32opls_140 0.0 12 HE33opls_140 0.0 13 CE1opls_145 0.0 32 HE1opls_146 0.0 33 CE2opls_145 0.0 34 HE2opls_146 0.0 35 [bonds] CE3 HE31 CE3 HE32 CE3 HE33 CE1 HE1 CE2 HE2 Relevant HDB lines: 3 4 HE3 CE3 SD CG1 1 1 HE1 CE1 CD1 CZ 1 1 HE2 CE2 CD2 CZ I thought this would cover everything, but I am receiving the following sort of error from pdb2gmx for each of the the three CE3 hydrogens(pdb2gmx -f 2H5Q.pdb -o 2H5Q_processed.gro -water tip3): "WARNING: atom HE31 is missing in residue CH6 66 in the pdb file You might need to add atom HE31 to the hydrogen database of building block CH6 in the file aminoacids.hdb (see the manual)" I've looked at other examples in the aminoacids.hdb file and cannot figure out what I am missing here, it seems like my hdb rule should be adding 3 type 4 hydrogens named HE31, HE32, and HE33. I am assuming that the other hdb rules are OK, since they seemed to work fine before, as indicated by examining the gro file. I would sincerely appreciate any help you can offer. Thank you! -Nathan -- -- J. Nathan Scott, Ph.D. Postdoctoral Fellow Department of Chemistry and Biochemistry Montana State University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Question about adding hydrogens to a newly constructed residue
On Sun, Sep 4, 2011 at 11:51 AM, Mark Abraham wrote: > On 5/09/2011 3:30 AM, J. Nathan Scott wrote: > >> Hello fellow GROMACS users, >> >> I am in the process of constructing a new residue in the OPLS-AA force >> field for the mCherry chromophore. However, I am having some difficulty in >> adding three CH3 hydrogens. In the 2H5Q PDB structure the chromophore >> residue, CH6, has CE1 and CE2 ring carbons defined, but also an extended >> chain carbon named CE. The problem is that my hdb rules were assigning HE1 >> and HE2 to the ring carbon hydrogens (1 1 HE1 CE1 CD1 >> CZ for example), and HE1, HE2, and HE3 to the CE carbon hydrogens (3 >> 4 HE CE SD CG1). Since these hydrogens are of different >> types, I need to have them named distinctly in my RTP file and need for >> Gromacs to understand them as different types. I changed the CH6 residue's >> CE atom to CE3 in the PDB file and the relevant RTP entries accordingly (see >> below). I also changed the hdb entry for the new CE3 atom (also below). >> >> Relevant RTP lines: >> CE3opls_209 0.0 10 >> HE31opls_140 0.0 11 >> HE32opls_140 0.0 12 >> HE33opls_140 0.0 13 >> CE1opls_145 0.0 32 >> HE1opls_146 0.0 33 >> CE2opls_145 0.0 34 >> HE2opls_146 0.0 35 >> [bonds] >> CE3 HE31 >> CE3 HE32 >> CE3 HE33 >> CE1 HE1 >> CE2 HE2 >> >> Relevant HDB lines: >> 3 4 HE3 CE3 SD CG1 >> 1 1 HE1 CE1 CD1 CZ >> 1 1 HE2 CE2 CD2 CZ >> >> I thought this would cover everything, but I am receiving the following >> sort of error from pdb2gmx for each of the the three CE3 hydrogens(pdb2gmx >> -f 2H5Q.pdb -o 2H5Q_processed.gro -water tip3): >> >> "WARNING: atom HE31 is missing in residue CH6 66 in the pdb file >> You might need to add atom HE31 to the hydrogen database of >> building block CH6 >> in the file aminoacids.hdb (see the manual)" >> >> I've looked at other examples in the aminoacids.hdb file and cannot figure >> out what I am missing here, it seems like my hdb rule should be adding 3 >> type 4 hydrogens named HE31, HE32, and HE33. I am assuming that the other >> hdb rules are OK, since they seemed to work fine before, as indicated by >> examining the gro file. I would sincerely appreciate any help you can offer. >> Thank you! >> > > I can't see a reason why that wouldn't work. However, there's no need for > you to preserve the PDB atom name for CE. Reducing the potential for some > atom-naming screw-up such as this is a good reason to change it (in both > your coordinate file and .rtp entry). It will probably just work, or at the > very least simplify further trouble-shooting. > > Mark > Hello Mark, thank you for your help, but I took your very reasonable advice and am still receiving the exact same sort of error. I changed the PDB file atom name to CQ, which of course makes it unique within that residue (and indeed in the whole PDB file). I updated my .rtp entries and the .hdb rules accordingly, and yet I still receive the exact same sort of error. It seems as if something is wrong with my hdb syntax, but having looked at numerous other examples in the hdb file and online I am at a loss as to what the problem might be. For what it's worth, if I use the -missing switch when I run pdb2gmx, the other CH6 hydrogen atoms appear to be added correctly in the resulting gro file, with the names exactly as I expected from the hdb naming rules. My input: pdb2gmx -f 2H5Q_spdbv.pdb -o 2H5Q_processed.gro -water tip3 Error received: "WARNING: atom HQ1 is missing in residue CH6 66 in the pdb file You might need to add atom HQ1 to the hydrogen database of building block CH6 in the file aminoacids.hdb (see the manual)" "WARNING: atom HQ2 is missing in residue CH6 66 in the pdb file You might need to add atom HQ1 to the hydrogen database of building block CH6 in the file aminoacids.hdb (see the manual)" "WARNING: atom HQ3 is missing in residue CH6 66 in the pdb file You might need to add atom HQ1 to the hydrogen database of building block CH6 in the file aminoacids.hdb (see the manual)" PDB file: ATOM493 CQ CH6 A 66 42.848 20.230 6.798 1.00 40.19 hdb file: CH6 9 2 6 HG1 CG1 SD CB1 2 6 HB1 CB1 CG1 CA1 2 6 HA3 CA3 C3 N3 1 1 HB2 CB2 CA2 CG2 1
Re: [gmx-users] Question about adding hydrogens to a newly constructed residue
On Mon, Sep 5, 2011 at 9:29 AM, Mark Abraham wrote: > On 6/09/2011 1:22 AM, J. Nathan Scott wrote: > > > > On Sun, Sep 4, 2011 at 11:51 AM, Mark Abraham wrote: > >> On 5/09/2011 3:30 AM, J. Nathan Scott wrote: >> >>> Hello fellow GROMACS users, >>> >>> I am in the process of constructing a new residue in the OPLS-AA force >>> field for the mCherry chromophore. However, I am having some difficulty in >>> adding three CH3 hydrogens. In the 2H5Q PDB structure the chromophore >>> residue, CH6, has CE1 and CE2 ring carbons defined, but also an extended >>> chain carbon named CE. The problem is that my hdb rules were assigning HE1 >>> and HE2 to the ring carbon hydrogens (1 1 HE1 CE1 CD1 >>> CZ for example), and HE1, HE2, and HE3 to the CE carbon hydrogens (3 >>> 4 HE CE SD CG1). Since these hydrogens are of different >>> types, I need to have them named distinctly in my RTP file and need for >>> Gromacs to understand them as different types. I changed the CH6 residue's >>> CE atom to CE3 in the PDB file and the relevant RTP entries accordingly (see >>> below). I also changed the hdb entry for the new CE3 atom (also below). >>> >>> Relevant RTP lines: >>> CE3opls_209 0.0 10 >>> HE31opls_140 0.0 11 >>> HE32opls_140 0.0 12 >>> HE33opls_140 0.0 13 >>> CE1opls_145 0.0 32 >>> HE1opls_146 0.0 33 >>> CE2opls_145 0.0 34 >>> HE2opls_146 0.0 35 >>> [bonds] >>> CE3 HE31 >>> CE3 HE32 >>> CE3 HE33 >>> CE1 HE1 >>> CE2 HE2 >>> >>> Relevant HDB lines: >>> 3 4 HE3 CE3 SD CG1 >>> 1 1 HE1 CE1 CD1 CZ >>> 1 1 HE2 CE2 CD2 CZ >>> >>> I thought this would cover everything, but I am receiving the following >>> sort of error from pdb2gmx for each of the the three CE3 hydrogens(pdb2gmx >>> -f 2H5Q.pdb -o 2H5Q_processed.gro -water tip3): >>> >>> "WARNING: atom HE31 is missing in residue CH6 66 in the pdb file >>> You might need to add atom HE31 to the hydrogen database of >>> building block CH6 >>> in the file aminoacids.hdb (see the manual)" >>> >>> I've looked at other examples in the aminoacids.hdb file and cannot >>> figure out what I am missing here, it seems like my hdb rule should be >>> adding 3 type 4 hydrogens named HE31, HE32, and HE33. I am assuming that the >>> other hdb rules are OK, since they seemed to work fine before, as indicated >>> by examining the gro file. I would sincerely appreciate any help you can >>> offer. Thank you! >>> >> >> I can't see a reason why that wouldn't work. However, there's no need >> for you to preserve the PDB atom name for CE. Reducing the potential for >> some atom-naming screw-up such as this is a good reason to change it (in >> both your coordinate file and .rtp entry). It will probably just work, or at >> the very least simplify further trouble-shooting. >> >> Mark >> > > Hello Mark, thank you for your help, but I took your very reasonable advice > and am still receiving the exact same sort of error. I changed the PDB file > atom name to CQ, which of course makes it unique within that residue (and > indeed in the whole PDB file). I updated my .rtp entries and the .hdb rules > accordingly, and yet I still receive the exact same sort of error. It seems > as if something is wrong with my hdb syntax, but having looked at numerous > other examples in the hdb file and online I am at a loss as to what the > problem might be. For what it's worth, if I use the -missing switch when I > run pdb2gmx, the other CH6 hydrogen atoms appear to be added correctly in > the resulting gro file, with the names exactly as I expected from the hdb > naming rules. > > > My input: > pdb2gmx -f 2H5Q_spdbv.pdb -o 2H5Q_processed.gro -water tip3 > > Error received: > "WARNING: atom HQ1 is missing in residue CH6 66 in the pdb file > You might need to add atom HQ1 to the hydrogen database of > building block CH6 > in the file aminoacids.hdb (see the manual)" > > "WARNING: atom HQ2 is missing in residue CH6 66 in the pdb file > You might need to add atom HQ1 to the hydrogen database of > building block CH6 > in the file aminoacids.hdb (see th
[gmx-users] Updating charges on-the-fly
Hello fellow GMX users, I've been digging in the archives and haven't yet found a good response to this question, so I thought I'd ask again, since I see from a post just last month others are still interested in this subject as well. Is it possible in Gromacs to periodically update/change the charges on a given molecule or residue during the course of a simulation? What I am envisioning is having a production simulation running, and then every "x" amount of time, the current checkpoint file gets read and processed by an external routine that calculates charges on the residue or molecule of interest, which are then fed back into Gromacs to continue the run. Is it possible to execute an external program from within a Gromacs simulation? I know this functionality must be in there somewhere, since Gromacs can communicate with external QM software, but I'm not sure if a charge modification scheme could make use of the same built-in I/O methods. Is such a scheme possible? I realize an alternative method would be to stop the run, do some calculation to recalculate the charges, and then perhaps use some simple code to modify the .top file directly, and finally grompp out a new tpr file and continue the run. Lather, rinse, repeat. I'm guessing this could be rather slow because of needing to call grompp over and over and the need to continually restart the simulation. For what it's worth, my interest lies mainly in excited state chromophores and I'd be using modified ZINDO code to calculate charges every x number of steps. This calculation is *very* fast, even for large chromophores, therefore my focus on other performance bottlenecks. I would be extremely grateful for any feedback on this subject, particularly from anyone who has done a similar thing successfully and cares to share any tips or code. -- -- J. Nathan Scott, Ph.D. Postdoctoral Fellow Department of Chemistry and Biochemistry Montana State University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] AMOEBA/AMBER 11 in Gromacs?
Hello Gromacs users, I was wondering, have the AMBER 11 and/or AMOEBA force fields been implemented by anyone for use in Gromacs? The reason I ask is that we are very interested in trying some of our simulations using the AMOEBA force field but would like to stick with the Gromacs engine if at all possible. Thanks in advance for any insight you can provide. Best Wishes, -- J. Nathan Scott, Ph.D. Postdoctoral Fellow Department of Chemistry and Biochemistry Montana State University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Re: gmx-users Digest, Vol 79, Issue 152
On Tue, Nov 23, 2010 at 9:55 AM, wrote: > J. Nathan Scott skrev 2010-11-23 17.35: >> Hello Gromacs users, >> >> I was wondering, have the AMBER 11 and/or AMOEBA force fields been >> implemented by anyone for use in Gromacs? The reason I ask is that we >> are very interested in trying some of our simulations using the AMOEBA >> force field but would like to stick with the Gromacs engine if at all >> possible. >> >> Thanks in advance for any insight you can provide. >> >> Best Wishes, >> >> -- >> J. Nathan Scott, Ph.D. >> Postdoctoral Fellow >> Department of Chemistry and Biochemistry >> Montana State University > > AMOEBA uses a type of point diopoles (iirc) that are not implemented in > gromacs. > > Cheers, > > -- > --- > Erik Marklund, PhD student > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: +46 18 471 4537 fax: +46 18 511 755 > er...@xray.bmc.uu.se http://folding.bmc.uu.se/ > Thanks for the confirmation of what I had already come to suspect, Eric. Best Wishes, -- -- J. Nathan Scott, Ph.D. Postdoctoral Fellow Department of Chemistry and Biochemistry Montana State University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Trouble with Gromacs finding the files it needs
Hello Gromacs users, I am having some difficulties with Gromacs finding the files it needs (at least that is what I *think* is the problem) and am hoping that someone can offer some insight. Using another user's home directory installation of Gromacs (v 4.0.7) I was able to work my way through Justin Lemkul's very nice lysozyme tutorial. However, now that I am working from my own home directory installation of Gromacs (v 4.5.3) I keep running into problems involving the addition of chloride ions in that same tutorial (as well as in other applications). The error I'm receiving using the newer version and installation of Gromacs occurs when I am using grommp to prepare a file containing protein, solvent, and ions for energy minimization: --- Program grompp, VERSION 4.5.3 Source code file: toppush.c, line: 1987 Fatal error: No such moleculetype CL- For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- This is very confusing since all I am doing is using a newer installation of Gromacs and following the exact same commands from the tutorial. Naturally I started checking and comparing topology files from the 2 runs to see if I could figure out what was going on. I noticed a few differences but am unsure what to make of them. The older version of Gromacs, for instance, has the user and host names correct at the top of the topology file, whereas my freshly installed version has both user and host as "onbekend", so it seems that user and host information is not being communicated in my new copy of Gromacs. Also, the topology file generated by the older version has includes of the form of #include "ffoplsaa.itp", #include "posre.itp", #include "spce.itp", and #include "ions.itp" whereas the newer version has includes of the form #include "oplsaa.ff/forcefield.itp", #include "posre.itp", #include "oplsaa.ff/spce.itp", and #include "oplsaa.ff/ions.itp". I know of course that "CL-" is the correct form of the chloride ion in OPLSAA (I checked oplsaa.ff/ions.itp to be certain), so I am quite baffled as to why this error is occurring. Is this indeed some sort of path problem, perhaps? I have noted that when I use "CL" instead of "CL-" in genion grommp has no trouble, but I believe it *should* because I have selected the OPLSAA forcefield. I have also noted that when I replace "oplsaa.ff/ions.itp" in my topology file with just "ions.itp" grommp runs fine, but this worries because I don't know why it works. In case it makes any difference, I installed Gromacs using the following procedure to yield MPI single and double precision versions of mdrun and single and double precision non-MPI versions of the tools: ./configure --enable-mpi --disable-float --prefix=/home/scott/gromacs --program-suffix=_mpi_d make mdrun && make install-mdrun make distclean ./configure --enable-mpi --enable-float --prefix=/home/scott/gromacs --program-suffix=_mpi make mdrun && make install-mdrun make distclean ./configure --disable-float --prefix=/home/scott/gromacs --program-suffix=_d make && make install make distclean ./configure --enable-float --prefix=/home/scott/gromacs make && make install Thank you very much for any help you can provide, this problem really has me scratching my head! -- J. Nathan Scott, Ph.D. Postdoctoral Fellow Department of Chemistry and Biochemistry Montana State University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Trouble with Gromacs finding the files it needs
On Tue, Nov 30, 2010 at 2:13 PM, Justin A. Lemkul wrote: > > > J. Nathan Scott wrote: >> >> Hello Gromacs users, >> >> I am having some difficulties with Gromacs finding the files it needs >> (at least that is what I *think* is the problem) and am hoping that >> someone can offer some insight. Using another user's home directory >> installation of Gromacs (v 4.0.7) I was able to work my way through >> Justin Lemkul's very nice lysozyme tutorial. However, now that I am >> working from my own home directory installation of Gromacs (v 4.5.3) I >> keep running into problems involving the addition of chloride ions in >> that same tutorial (as well as in other applications). The error I'm >> receiving using the newer version and installation of Gromacs occurs >> when I am using grommp to prepare a file containing protein, solvent, >> and ions for energy minimization: >> --- >> Program grompp, VERSION 4.5.3 >> Source code file: toppush.c, line: 1987 >> >> Fatal error: >> No such moleculetype CL- >> For more information and tips for troubleshooting, please check the >> GROMACS >> website at http://www.gromacs.org/Documentation/Errors >> --- >> >> This is very confusing since all I am doing is using a newer >> installation of Gromacs and following the exact same commands from the >> tutorial. Naturally I started checking and comparing topology files >> from the 2 runs to see if I could figure out what was going on. I >> noticed a few differences but am unsure what to make of them. >> >> The older version of Gromacs, for instance, has the user and host >> names correct at the top of the topology file, whereas my freshly >> installed version has both user and host as "onbekend", so it seems >> that user and host information is not being communicated in my new >> copy of Gromacs. Also, the topology file generated by the older >> version has includes of the form of #include "ffoplsaa.itp", #include >> "posre.itp", #include "spce.itp", and #include "ions.itp" whereas the >> newer version has includes of the form #include >> "oplsaa.ff/forcefield.itp", #include "posre.itp", #include >> "oplsaa.ff/spce.itp", and #include "oplsaa.ff/ions.itp". >> >> I know of course that "CL-" is the correct form of the chloride ion in >> OPLSAA (I checked oplsaa.ff/ions.itp to be certain), so I am quite >> baffled as to why this error is occurring. Is this indeed some sort of >> path problem, perhaps? I have noted that when I use "CL" instead of >> "CL-" in genion grommp has no trouble, but I believe it *should* >> because I have selected the OPLSAA forcefield. I have also noted that >> when I replace "oplsaa.ff/ions.itp" in my topology file with just >> "ions.itp" grommp runs fine, but this worries because I don't know why >> it works. >> > > The directory structure has changed as of version 4.5, and ion names have > been standardized across the force fields. The proper [moleculetype] of the > chloride ion (in oplsaa.ff/ions.itp) is indeed "CL" while the *residue name* > is "CL-" and the atom name (which is what you pass to genion) is "CL." > > So, if you have added a line like > > CL- 8 > > in the [molecules] directive of your topology (like in my tutorial), then > you get the fatal error. The [moleculetype] name is what you enter here, > not the residue name. > > I haven't updated my tutorial for version 4.5.x, but perhaps I should. If > you follow what I say exactly, you will have problems in the newer version. > > -Justin > Ahhh, now it all makes sense! Thanks very much for your helpful answer Justin! By the way, should I be concerned about "onbekend" in the user and server names? I don't particularly care what is in those fields, but am slightly worried that they indicate I have something configured incorrectly, which could then affect the functionality of the software. -Nathan >> In case it makes any difference, I installed Gromacs using the >> following procedure to yield MPI single and double precision versions >> of mdrun and single and double precision non-MPI versions of the >> tools: >> >> ./configure --enable-mpi --disable-float --prefix=/home/scott/gromacs >> --program-suffix=_mpi_d >> make mdrun && make install-mdrun >> make distclean >> >> ./configure --
[gmx-users] Replacing charges of a residue, pdb2gmx -rtpo alternative?
Hello all! I spent some time searching the archive and can't find an answer to this question. Is there a replacement for the -rtpo option for pdb2gmx? This option is mentioned in the v 4.5.3 (the version I am using) manual (pg 115) but does not seem to work, and yields the error "Invalid command line argument: -rtpo" when I try to use it I would basically like to have the OPLSAA aminoacids.rtp file in my working directory (which has some modified charges for the TRP residue) supersede the one in the Gromacs force field share directory. Is there a way to do this? So far I have resorted to copying the shared oplsaa.ff folder to my working directory and modifying the aminoacids.rtp file in that directory, and then selecting that directory to source my force field when I run pdb2gmx. This of course works, but I have noted a peculiar behavior using this method. No matter whether I select force field 1, which is OPLSAA from my working directory, or force field 15, which is OPLSAA from the share directory, my topology file ends up with charges in the working directory oplsaa.ff folder's aminoacids.rtp file. Even when I select that pdb2gmx should use the share version, it is clearly still using the force field folder in my working directory. I confirmed this by renaming the aminoacids.rtp in the working directory file to aminoacids.rtp.bak, which produced the error "Could not find any files ending on '.rtp' in the force field directory 'oplsaa.ff'" Can someone recommend a better method for what I am attempting to do? Also, is pdb2gmx's handling of force field directories appropriate? I had assumed that selecting the share version of a force field would force all the necessary files to be read from that share directory, but this is clearly not the case. -- -- J. Nathan Scott, Ph.D. Postdoctoral Fellow Department of Chemistry and Biochemistry Montana State University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Replacing charges of a residue, pdb2gmx -rtpo alternative?
On Tue, Dec 7, 2010 at 3:17 PM, Mark Abraham wrote: > On 8/12/2010 4:07 AM, J. Nathan Scott wrote: >> >> Hello all! I spent some time searching the archive and can't find an >> answer to this question. Is there a replacement for the -rtpo option >> for pdb2gmx? This option is mentioned in the v 4.5.3 (the version I am >> using) manual (pg 115) but does not seem to work, and yields the error >> "Invalid command line argument: -rtpo" when I try to use it >> >> I would basically like to have the OPLSAA aminoacids.rtp file in my >> working directory (which has some modified charges for the TRP >> residue) supersede the one in the Gromacs force field share directory. >> Is there a way to do this? >> >> So far I have resorted to copying the shared oplsaa.ff folder to my >> working directory and modifying the aminoacids.rtp file in that >> directory, and then selecting that directory to source my force field >> when I run pdb2gmx. > > This is the intended behaviour. Rather than modifying your installed > database, or having to mess with the GMXLIB environment variable, you can > copy the whole xx.ff directory into a local directory and have local > modifications. pdb2gmx reports clearly on stdout which directory(s) it is > (considering) using. > >> This of course works, but I have noted a peculiar >> behavior using this method. No matter whether I select force field 1, >> which is OPLSAA from my working directory, or force field 15, which is >> OPLSAA from the share directory, my topology file ends up with charges >> in the working directory oplsaa.ff folder's aminoacids.rtp file. Even >> when I select that pdb2gmx should use the share version, it is clearly >> still using the force field folder in my working directory. I >> confirmed this by renaming the aminoacids.rtp in the working directory >> file to aminoacids.rtp.bak, which produced the error "Could not find >> any files ending on '.rtp' in the force field directory 'oplsaa.ff'" > > That sounds very weird. I'd suggest you start a new working directory, copy > the oplsaa.ff over fresh, make the .rtp modifications and see if you can > reproduce the issue. If so, please file a Bugzilla. Thanks for your reply Mark. I have confirmed this behavior many times now, and so I have filed a Bugzilla report as you suggested. I did find a quick fix: as long as the copy of the .ff directory in the working directory is named something different than the copy in share/top then pdb2gmx seems to differentiate between the two perfectly well, as confirmed by the charges in the topology files it is generating. It is only when they are named the same thing (oplsaa.ff, for instance) that the force field selection problem happens. Perhaps the programmers assumed users would be smart enough to rename the modified force field directory? ;) Best Wishes, -Nathan > >> Can someone recommend a better method for what I am attempting to do? >> Also, is pdb2gmx's handling of force field directories appropriate? I >> had assumed that selecting the share version of a force field would >> force all the necessary files to be read from that share directory, >> but this is clearly not the case. > > It should be the case. > > 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/Support/Mailing_Lists/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/Support/Mailing_Lists > -- -- J. Nathan Scott, Ph.D. Postdoctoral Fellow Department of Chemistry and Biochemistry Montana State University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Seeking advice on how to build Gromacs on Teragrid resources
ssi, D. Donadio and M. Parrinello Canonical sampling through velocity rescaling J. Chem. Phys. 126 (2007) pp. 014101 --- Thank You --- --- My PBS error file is not of much help either I fear, an example of such a file is pasted below: --- stty: standard input: Invalid argument stty: standard input: Invalid argument NNODES=16, MYRANK=0, HOSTNAME=abe0828 NNODES=16, MYRANK=2, HOSTNAME=abe0828 NNODES=16, MYRANK=12, HOSTNAME=abe0828 NNODES=16, MYRANK=4, HOSTNAME=abe0828 NNODES=16, MYRANK=10, HOSTNAME=abe0828 NNODES=16, MYRANK=8, HOSTNAME=abe0828 NNODES=16, MYRANK=6, HOSTNAME=abe0828 NNODES=16, MYRANK=14, HOSTNAME=abe0828 NODEID=0 argc=17 NODEID=2 argc=17 NODEID=4 argc=17 NODEID=10 argc=17 NODEID=12 argc=17 NODEID=6 argc=17 NODEID=14 argc=17 NODEID=8 argc=17 NNODES=16, MYRANK=5, HOSTNAME=abe0825 NNODES=16, MYRANK=13, HOSTNAME=abe0825 :-) G R O M A C S (-: NNODES=16, MYRANK=9, HOSTNAME=abe0825 NNODES=16, MYRANK=11, HOSTNAME=abe0825 Great Red Oystrich Makes All Chemists Sane :-) VERSION 4.5.3 (-: Back Off! I just backed up nvt.log to ./#nvt.log.2# Reading file nvt.tpr, VERSION 4.5.3 (single precision) Will use 10 particle-particle and 6 PME only nodes This is a guess, check the performance at the end of the log file Making 2D domain decomposition 2 x 5 x 1 Back Off! I just backed up nvt.edr to ./#nvt.edr.2# -- The non-Torque section of the PBS log file is below: --- Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. running mpdallexit on abe0828 LAUNCHED mpd on abe0828 via RUNNING: mpd on abe0828 LAUNCHED mpd on abe0825 via abe0828 RUNNING: mpd on abe0825 abe0828_43972 (10.1.67.66) abe0825_37571 (10.1.67.63) rank 1 in job 1 abe0828_43972 caused collective abort of all ranks exit status of rank 1: killed by signal 9 rank 0 in job 1 abe0828_43972 caused collective abort of all ranks exit status of rank 0: killed by signal 9 - I would should also note that both .edr and .trr files are created in the working directory, but both files are 0 bytes. Like I said, I realize this question is perhaps a bit off the topic of Gromacs exclusively, but I hope that someone can offer some tips or spot any obvious problems with my method that I have not noticed and would sincerely appreciate any help you can offer a novice. Best Wishes, -Nathan -- J. Nathan Scott, Ph.D. Postdoctoral Fellow Department of Chemistry and Biochemistry Montana State University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Seeking advice on how to build Gromacs on Teragrid resources
On Thu, Dec 9, 2010 at 3:38 PM, Mark Abraham wrote: > On 10/12/2010 9:14 AM, J. Nathan Scott wrote: >> >> Hello gmx users! I realize this may be a touch off topic, but I am >> hoping that someone out there can offer some advice on how to build >> Gromacs for parallel use on a Teragrid site. Our group is currently >> using Abe on Teragrid, and unfortunately the latest version of Gromacs >> compiled for public use on Abe is 4.0.2. Apparently installation of >> 4.5.3 is at least on the to-do list for Abe, but we would very much >> like to use 4.5.3 now if we can get this issue figured it out. >> >> I have built a parallel version of mdrun using Abe installed versions >> of fftw3 and mvapich2 using the following commands: > > Certainly MPICH use is discouraged, as GROMACS seems to find some bugs in > it. I'm not sure about MVAPICH. Certainly you should be sure to be using the > latest version. Compare with OpenMPI if you can. Mark, thank you very much for the tip, it turns out the problem was my choice of using the MVAPICH2 1.2 libraries/includes for compilation. Switching to Open MPI 1.3.2 appears to have solved everything and mdrun is now running quite well on multiple nodes on Abe. Thank you again for the suggestion! Best Wishes, -Nathan >> setenv CPPFLAGS "-I/usr/apps/math/fftw/fftw-3.1.2/gcc/include/ >> -I/usr/apps/mpi/marmot_mvapich2_intel/include" >> setenv LDFLAGS "-L/usr/apps/math/fftw/fftw-3.1.2/gcc/lib >> -L/usr/apps/mpi/marmot_mvapich2_intel/lib" >> ./configure --enable-mpi --enable-float --prefix=/u/ac/jnscott/gromacs >> --program-suffix=_mpi >> make -j 8 mdrun&& make install-mdrun >> >> My PBS script file looks like the following: >> >> --- >> #!/bin/csh >> #PBS -l nodes=2:ppn=8 > > Simplify the conditions when trying to diagnose a problem - try to run on > one 8-processor node, or even 1 processor. Your crash is consistent with > some MPI problem, because (off the top of my head) it seems to happen when > GROMACS starts to do communication to pass around the input data. > > Mark > -- -- J. Nathan Scott, Ph.D. Postdoctoral Fellow Department of Chemistry and Biochemistry Montana State University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
