[gmx-users] Gibbs Energy Calculation and charges

Dear Dallas: Seems like you could test Michael's idea by removing all 1-4 NB interactions from your topology. It won't produce any biologically useful results, but might be a worthwhile check to see if indeed this is the issue. To do this, I figure you would set gen-pairs to "no" in the [ defau

[gmx-users] 2D umbrella sampling simulation

unfortunately not. It will be done eventually though: to follow the progress of that feature, check out: http://redmine.gromacs.org/issues/1346 If you have to do that, there is a patch that I posted on that same redmine page (posts 8 and 9) to allow this in gromacs 4.0.5. Chris. -- original me

[gmx-users] 2D umbrella sampling simulation

Your restraint involving group C should use pull_group2, etc, not another copy of pull_group1. Other than that, it looks like a valid approach. Chris. -- original message -- I am going to perform the two-dimensional umbrella sampling using a pair of distances (the distance btw atoms A and

[gmx-users] default -rdd with distance restraints seems too large

Thanks for the hint XAvier. Unfortunately, I get crashes with particle decomposition (see below). If I use either DD or PD, I can run on up to 2 threads without adjusting -rdd or -dds. I can only use >2 thread with DD if I set -rdd 2.8. If I try to use more than 2 threads with PD, I get lincs

[gmx-users] default -rdd with distance restraints seems too large

Indeed, sorry that I didn't notice that, Mark. Looks as if the two-body bonded interaction gets multiplied by 1.1/0.8 so I suppose that this is working as it should. It's a shame that long distance restraints limit the parallalization so much, but it is understandable. Thanks for helping me wit

[gmx-users] default -rdd with distance restraints seems too large

I have a system that also uses a set of distance restraints The box size is: 7.12792 7.12792 10.25212 When running mdrun -nt 8, I get: Fatal error: There is no domain decomposition for 8 nodes that is compatible with the given box and a minimum cell size of 3.62419 nm However, the larges

[gmx-users] Gibbs Energy Calculation and charges

Ah, I see. I guess that you are using couple-intramol = no (the default in v4.6.3 at least). That means that the intramolecular charge-charge interactions are always at full-strength (and therefore different). I would expect that normal at lambda=0 should be the same as double at lambda=0.5 onl

[gmx-users] Gibbs Energy Calculation and charges

Dear Dallas: Am I correct that you are saying that for both the regular-charge and double-charge solute molecule, you decoupled the solvent-solute charge-charge interactions and expected that the dH/dL and overall free energy values of the double-charge solute would be exactly two times the

[gmx-users] Gromacs on Stampede

Why not put it in a slurm script and submit that script as a (probably single-node) job. It is not generally acceptable to use a large fraction of the head node of a shared resource for a substantial amount of time. If your problem is different and of a gromacs nature, you may need to describe

[gmx-users] Gromacs on Stampede

Dear Arun: here is how I compile fftw and gromacs on stampede. I have also included a job script and a script to submit a chain of jobs. As Szilárd notes, this does not use the MICs, but it is still a rather fast machine. # Compilation for single precision gromacs plus mdrun_mpi # #

[gmx-users] how to calculate kinetic constant?

f you do this for different temperatures, you can back out the activation energy and hence the rate constant. I would love to learn more about this. Any inputs will be welcome. Regards, On Sat, Oct 5, 2013 at 11:44 PM, Christopher Neale < chris.neale at mail.utoronto.ca> wrote: > If you

[gmx-users] how to calculate kinetic constant?

If you want K_on and K_off, then I think you need to look at long-time equilibrium simulations or massively repeated simulations connected with a MSM. Beyond that, I believe that you will need to understand all of the important free energy barriers in all degrees of freedom (hard, to say the lea

[gmx-users] pull-code constant-force direction gives unexpected error about distance larger than box size

Commenting out the gmx_fatal() call in src/mdlib/pull.c, line: 331 and recompiling grompp and mdrun allows the run to proceed. Everything is stable for 250 ps. I will report if it fails. I have posted a redmine at: http://redmine.gromacs.org/issues/1352 Thank you, Chris. -- original message --

[gmx-users] pull-code constant-force direction gives unexpected error about distance larger than box size

Dear Users: I am trying to use the pull code to add a constant force in a particular direction. I am getting an error that the initial distance is greater than 1/2 the box size. (error in 4.5.5, 4.6.1, 4.6.3) I must not understand how to use this. I checked the online .mdp options: http://manua

[gmx-users] Membrane is shifted a lot during umbrella sampling

Dear Sudipta: on average, bilayers migrate along the positive z axis during gromacs simulations with a variety of atomistic force fields. This has been reported before, but never fully resolved ( http://redmine.gromacs.org/issues/165 suggests it is due to rounding ) and I see it all the time. I

[gmx-users] OPLS/AA + TIP5P, anybody?

Dear Grzegorz: >From a quick look at your .mdp, I also suggest that you go back to your system >including the peptide that you had managed to finish EM with modified flexible >tip5p but then crashed with the standard rigid tip5p during MD and try the MD >again using gen-vel = yes if you're sti

[gmx-users] OPLS/AA + TIP5P, anybody?

steep steps, but all the 5624 distances were rock solid 0.7A, as expected. I still did not post the redmine issue, I want to be sure that I am doing everything correctly. On 2013-09-29 18:47, Christopher Neale wrote: > Dear Grzegorz: > > Under no conditions should any of the tip5p geomet

[gmx-users] OPLS/AA + TIP5P, anybody?

Dear Grzegorz: Under no conditions should any of the tip5p geometry change (for the standard tip5p model). If you find that this is happening, then that is certainly an error. You can check if you like by analyzing your trajectory. However, flexible bonds will allow the distance from the argi

[gmx-users] OPLS/AA + TIP5P, anybody?

Dear Gigo: that's a good comprehensive testing and report. Please let us know what you find out from those authors. Their paper was short on methods (unless I missed it... I didn't check for any SI), so perhaps they did something non-standard and didn't report it. I think at this point it is a

[gmx-users] OPLS/AA + TIP5P, anybody?

Dear Gigo: everything that I suggested was just ways that you might get a system without bad contacts to start your simulation with the proper (standard) tip5p model and oplsaa. I expected that combination to work together since they came out of the same lab, but looking at the initial tip5p pa

[gmx-users] OPLS/AA + TIP5P, anybody?

Dear Gigo: I've never used tip5p, but perhaps you could add some LJ terms to the opls_120 definition, do your minimization, then remove the fake LJ term on opls_120 and run your MD? If that doesn't work, then you might be able to minimize your system using FLEXIBLE tip3p water and then use a sc

[gmx-users] Membrane simulation with OPLS ff.

Dear Karthi: As far as I am aware, there is no OPLSAA lipid force field. I have used Berger lipids with OPLSAA protein ( http://www.pomeslab.com/files/lipidCombinationRules.pdf ) but that is mixing a UA lipid with an AA protein so be aware of possible problems arising out of that. Charmm has pr

[gmx-users] "Illegal instruction" error from alchemical-gromacs.py

Dear Users: I'm having difficulty running MBAR after some free energy calculations (MBAR via alchemical-gromacs.py obtained from alchemistry.org). The input options to alchemical-gromacs.py have obviously changed since the site at http://www.alchemistry.org/wiki/GROMACS_4.6_example:_Direct_etha

[gmx-users] segfault when running the alchemistry.org ethanol solvation free energy tutorial

Agreed, the following parameters do not segfault in single or double precision: sc-alpha = 0.5 sc-power = 1 sc-r-power = 6 Same goes for http://bugzilla.gromacs.org/issues/1306 The following parameters give a segfault in single precision but are ok in

[gmx-users] segfault when running the alchemistry.org ethanol solvation free energy tutorial

No, this is not the expanded ensemble version. It's the initial "Running the calculation with Gromacs" section straight out of http://www.alchemistry.org/wiki/GROMACS_4.6_example:_Direct_ethanol_solvation_free_energy I get the segfault with a single run (at any of the 9 individual lambda values)

[gmx-users] segfault when running the alchemistry.org ethanol solvation free energy tutorial

My mistake I still get a segfault even when using double precision. (EM doesn't help, nor does switching to Berendsen pressure coupling). Note that I can stop the segfault when running at init-lambda-state = 0 if I set: couple-lambda0 = none couple-lambda1 = none inste

[gmx-users] segfault when running the alchemistry.org ethanol solvation free energy tutorial

ysome. Thank you, Chris. -- original message -- I found the -multi version of that tutorial a bit temperamental... Michael Shirts suggested that double precision is more reliable for expanded ensemble. Hopefully he can chime in in a day or two. Mark On Thu, Sep 26, 2013 at 9:00 PM, Christopher

[gmx-users] segfault when running the alchemistry.org ethanol solvation free energy tutorial

Dear Users: Has anyone successfully run the free energy tutorial at http://www.alchemistry.org/wiki/GROMACS_4.6_example:_Direct_ethanol_solvation_free_energy ? I just tried it and I get a segmentation fault immediately (see output at the end of this post). I get a segfault with both 4.6.3 and

[gmx-users] BGQ compilation with verlet kernels: #include file "kernel_impl.h" not found.

Indeed, it works just fine when I compile with mpi. I never thought to check that. My usual procedure is to compile the whole package without mpi and then to compile mdrun with mpi. Thanks for the help Mark. Here is the compilation script that worked for me. module purge module load vacpp/12.1

[gmx-users] BGQ compilation with verlet kernels: #include file "kernel_impl.h" not found.

Dear Users: I am attempting to use the new BGQ kernels with the version of gromacs at https://gerrit.gromacs.org/#/c/2572/ , which I obtained by: git init git fetch https://gerrit.gromacs.org/gromacs refs/changes/72/2572/1 && git checkout FETCH_HEAD I then attempted to compile like this: modu

[gmx-users] charmm36 proteins

What is the charmm36 protein force field? (can you provide a reference to what you are referring to). As far as I know, there is no such thing as "charmm36" proteins. There are charmm27+cmap proteins (implemented in gromacs already) and charmm36 lipids (implemented in gromacs already). -- orig

[gmx-users] VDW switched off in CHARMM tip3p model

>From my inspection of the force field files included in gromacs-4.6.1, when you use the charmm ff and the charmm tip3p (tips3p.itp) you get the hydrogen type HT, which does have LJ on the hydrogen atoms, whereas you only get the hydrogen type HWT3 when you use the non-charmm tip3p (tip3p.itp).

[gmx-users] RE: Umbrella sampling question

Why not do two umbrella sampling simulations: one with initial conformations from your faster pulling and one with initial conformations from your slower pulling. Then you can run them both as regular US simulations until (a) neither US PMF is drifting systematically with increasing simulation t

[gmx-users] segfault with an otherwise stable system when I turn on FEP (complete decoupling)

solution. Thank you for your assistance. Chris. -- original message -- Chris, can you post a redmine on this so I can look at the files? Also, does it crash immediately, or after a while? On Thu, Jul 18, 2013 at 2:45 PM, Christopher Neale wrote: > Dear Users: > > I have a system with

[gmx-users] segfault with an otherwise stable system when I turn on FEP (complete decoupling)

Dear Users: I have a system with water and a drug (54 total atoms; 27 heavy atoms). The system is stable when I simulate it for 1 ns. However, Once I add the following options to the .mdp file, the run dies after a few ps with a segfault. free-energy = yes init-lambda = 1 couple-lambda0 = vdw-

[gmx-users] clarification of equation 4.65

Dear Users: can anybody confirm that there is a mistake in equation 4.65 on page 82 of the manual for version 4.6.1? Specifically, I think that the final term should be C4*(1-cos(4*theta)) and not C4*(1+cos(4*theta)) where the difference is the sign of the cosine term ? Thank you, Chris. -- gm

[gmx-users] cation-pi interaction

I've always wondered why people do this. There are no pi electrons in your force field so it seems to me that if you find a stable "cation-pi" interaction in your simulations then that just implies that a real cation-pi interaction is not necessary to stabilize this particular conformation. That

[gmx-users] Usage of g_spatial

Sounds like a trjconv problem, not a g_spatial problem to me. You should center only the group that makes sense for your SDF -- you probably want to pick a single cation for this (then, separately, do another run selecting a single anion; each will be used to generate a separate SDF). Then outp

[gmx-users] line wrapping on the gmx-users list

. However, I choose to receive digests, so I don't get those emails and thus can not reply to them. Thanks for your help. Chris. On Sat, May 11, 2013 at 5:15 AM, Christopher Neale < chris.neale at mail.utoronto.ca> wrote: > The lack of line-wrapping makes it a pain to read. It happen

[gmx-users] line wrapping on the gmx-users list

The lack of line-wrapping makes it a pain to read. It happens to my emails that are posted on this list (and I have seen others), unless I put explicit line-breaks in my posts, which I often forget to do. Is there anything that can be done? IMHP, this should be automatically handled, and I oft

[gmx-users] keeping water (entirely) out of the bilayer core

Dear Jianguo, XAvier, and Dallas: Thank you for your great suggestions. I am making progress, but still have not found an efficient way to do this. I don;t have any particular questions in this post, but wanted to provide an update and also to see if anybody has any additional ideas based on wha

[gmx-users] mdp-settings for charmm36 and lipid apl values

It is a really bad idea to use standard tip3p with charmm36 lipids (see the Piggot paper that you referenced and also Sapay, N. et al. 2010 J. Comp. Chem. 32, 1400-1410 + probably others). dt 0.001 with nstlist 5 seems like overkill on the nstlist update frequency (not a problem though). Here'

[gmx-users] Usage of g_spatial

See my previous response. You don't need a .tpr for trjconv (unless you are doing pbc operations). trjconv -h will also tell you that. Just use trjconv -s my.pdb Chris. -- original message -- Sorry for my ignorance, since the help manual uses tpr file for the first two steps before running g_s

[gmx-users] Usage of g_spatial

Try this: trjconv -s my.pdb -f my.pdb -o mymod.pdb g_spatial -s mymod.pdb -f mymod.pdb For the pre-processing, there must also be AMBER tools that will do this for you if for some reason the above does not work for you (e.g. Option -pbc mol requires a .tpr file for the -s option) Chris. -- or

[gmx-users] keeping water (entirely) out of the bilayer core

Thank you for the advice Jianguo. This seems like a good way forward. I was hoping not to have to learn how to use new software, but perhaps it is time. Thank you, Chris. -- original message -- Hi Chris, Perhaps you can try PLUMED+GROMACS. In that case, you can define a collective variable a

[gmx-users] keeping water (entirely) out of the bilayer core

potential that would apply to water molecules. I am not sure how it is called but it is available and described in the manual. On May 4, 2013, at 2:46, Christopher Neale wrote: > Dear users: > > I am interested in running simulations of lipid bilayers in which I keep all > water mole

[gmx-users] keeping water (entirely) out of the bilayer core

Dear users: I am interested in running simulations of lipid bilayers in which I keep all water molecules out of the bilayer core (not just statistically, but absolutely). However, I have been unable to figure out how to do it. I'll list what I have tried in the hope that others have some ideas

[gmx-users] How to rescue trr trajectory when two or more corrupted frames exist

This is great advice from Mark. If you don't get around to doing analysis frequently, then you can at least set up your run script to execute gmxcheck on all relevant files prior to each time you restart a run in which you load in a .cpt file and to error out if there is some corruption found.

[gmx-users] How to rescue trr trajectory when two or more corrupted frames exist

If the corrupted frame is at 1000 ps, and you can not get at the data after the corrupted frame by using: trjconv -b 1100 , then I suspect that you don't have any good solution here, unless the developers put in some type of magic number at the start of each frame that you could search for with

[gmx-users] Re: How to use multiple nodes, each with 2 CPUs and 3 GPUs

Dear Szilárd: Thank you for your assistance. I understand the importance of reading the documentation and I read it about 5 times before I posted to this list. In fact, it's kind of buried in my initial post, but I did run MPI gromacs with mpirun -np 3 the first time and it didn't work. I have

[gmx-users] How to use multiple nodes, each with 2 CPUs and 3 GPUs

Thank you Berk, I am still getting an error when I try with MPI compiled gromacs 4.6.1 and -np set as you suggested. I ran like this: mpirun -np 6 /nics/b/home/cneale/exe/gromacs-4.6.1_cuda/exec2/bin/mdrun_mpi -notunepme -deffnm md3 -dlb yes -npme -1 -cpt 60 -maxh 0.1 -cpi md3.cpt -nsteps 5000

[gmx-users] How to use multiple nodes, each with 2 CPUs and 3 GPUs

Dear Users: I am having trouble getting any speedup by using more than one node, where each node has 2 8-core cpus and 3 GPUs. I am using gromacs 4.6.1. I saw this post, indicating that the .log file output about number of gpus used might not be accurate: http://lists.gromacs.org/pipermail/gmx-

[gmx-users] position restraint and umbrella potential contribution to the virial

Dear users and developers: We have conducted some NPT umbrella sampling (US) simulations to investigate the free energy associate with the aproach of 2 alpha helical peptides. The order parameter is the Cartesian X dimension. During these simulations, in order to maintain (i) the structure of i

[gmx-users] amber99 with berger's lipids

Did you correctly account for the different 1-4 scaling factors in the Berger and Amber lipids (either by obtaining .itp files from the authors of the Berger lipids-Amber protein article or making the changes yourself)? If not, then you are doing your simulation incorrectly (see their paper for

[gmx-users] chiller failure leads to truncated .cpt and _prev.cpt files using gromacs 4.6.1

Thank you Berk, my problem, was indeed that I didn't have any valid .cpt files. The only way that I could proceed was to extract a frame from the .xtc file and run it through grompp again to get a new .tpr. That's fine and things are running again. I just wanted to pass all of this information a

[gmx-users] chiller failure leads to truncated .cpt and _prev.cpt files using gromacs 4.6.1

Thank you, Berk, Justin, and Matthew, for your assistance. I checked with my sysadmin, who said: The /global/scratch FS is Lustre. It is fully POSIX and the fsync etc are fully and well implemented. However when the 'power off' command is issued there is no way OS can finish I/O in a controlled

[gmx-users] Simulation membrane proteins in amber99 force field.

Dear James: As always, check the primary literature. The Amber99SB ff was introduced with an 8A cutoff and PME: http://www.ncbi.nlm.nih.gov/pubmed/16981200 Other cutoffs are at your discretion. I am, for instance, using this ff with a 1.0 nm cutoff and PME because I am using it with the Stockho

[gmx-users] chiller failure leads to truncated .cpt and _prev.cpt files using gromacs 4.6.1

Dear Matthew: Thank you for noticing the file size. This is a very good lead. I had not noticed that this was special. Indeed, here is the complete listing for truncated/corrupt .cpt files: -rw-r- 1 cneale cneale 1048576 Mar 26 18:53 md3.cpt -rw-r- 1 cneale cneale 1048576 Mar 26 18:54 m

[gmx-users] Hydrophobic contact cut-off

The standard approach in cases like this, assuming that you have some contacts at some point in your trajectory, is to use your trajectory to construct a radial distribution function (RDF) and then to define a "contact" as any interaction up to the minimum following the first maximum of the RDF.

[gmx-users] chiller failure leads to truncated .cpt and _prev.cpt files using gromacs 4.6.1

Dear Users: A cluster that I use went down today with a chiller failure. I lost all 16 jobs (running gromacs 4.6.1). For 13 of these jobs, not only is the .cpt file truncated, but also the _prev.cpt file is truncated, meaning that I am going to have to go back through the files, extract a frame

[gmx-users] Performance of 4.6.1 vs. 4.5.5

Dear users: I am seeing a 140% performance boost when moving from gromacs 4.5.5 to 4.6.1 when I run a simulation on a single node. However, I am "only" seeing a 110% performance boost when running on multiple nodes. Does anyone else see this? Note that I am not using the verlet cutoff scheme.

[gmx-users] Gromacs with Intel Xeon Phi coprocessors ?

Dear users: does anybody have any experience with gromacs on a cluster in which each node is composed of 1 or 2 x86 processors plus an Intel Xeon Phi coprocessor? Can gromacs make use of the xeon phi coprocessor? If not, does anybody know if that is in the pipeline? Thank you, Chris. -- gmx-us

[gmx-users] g_density fails after calculating for the last snapshot

What output do you get from gmxcheck -f martin_md_290K_100ns_tau1.xtc ? Also, can you extract that problematic frame with trjconv and run g_density on that one frame (what happens?). Also, can you make a new .xtc that is missing that last frame and see what g_density does? These will help you t

[gmx-users] Trouble restarting a 4.5.5 run with 4.6.1 (forced to use -noappend)

Dear Users, I have a system that has been running under gromacs 4.5.5. I can restart it fine from a checkpoint file with gromacs 4.5.5 but not with gromacs 4.6.1. The long description follows, but the short answer seems to be that 4.5.5 recorded My-X/Y/Z values (the internet tells me these rel

[gmx-users] how to get pdb2gmx to use an arbitrarily located forcefield.ff directory?

ginal message -- Hi Chris, I don't know if thngs changed in gromacs 4.6.x, but I succesfully did what you are triying to do setting the two variable GMXLIB and GMXDATA at the same time. Francesco 2013/3/5 Christopher Neale <[hidden email]> > Hello, > > I have downloaded the charmm

[gmx-users] how to get pdb2gmx to use an arbitrarily located forcefield.ff directory?

Hello, I have downloaded the charmm36.ff directory and would like to use it with pdb2gmx. Everything works fine if I put it in the current directory or the share/gromacs/top directory of the binary that I am using. However, I'd like to be able to put the charmm36.ff directory in an arbitrary pl

[gmx-users] The sum of the two largest charge group radii is larger than rlist - rvdw (because rlist < rvdw)

Dear Joakim: I've started bilayer simulations with both of the new conditions that you mentioned. Thank you for the advice ans references. I am surprised to hear that the bilayer features are similar with different vdw cutoffs (although I'll check also). Perhaps this is an unexpected win for di

[gmx-users] On the usage of SD integrator as the thermostat

integrator together with Nose-Hoover thermostat. Thanks, km. On Fri, Nov 23, 2012 at 5:43 PM, Christopher Neale wrote: > I use the SD integrator with tau_t = 1.0 ps for all of my work, including > proteins in aqueous solution > or embedded in a lipid membrane. > > Any value of ta

[gmx-users] On the usage of SD integrator as the thermostat

I use the SD integrator with tau_t = 1.0 ps for all of my work, including proteins in aqueous solution or embedded in a lipid membrane. Any value of tau-t is "correct", and none will give you the proper dynamics, but I find that the diffusion of both water and lipids is quite reasonable when usi

[gmx-users] REMD simulation

Xavier is right, except that you can also reduce the size of your system. You can take larger steps in temperature if you have fewer atoms. If you are using a cubic system, you can move to a rhombic dodecahedron. Even constraining all bonds will help a bit here (vs. harmonic bonds). There are

[gmx-users] Re: Umbrella sampling question

What you reported is not what you did. It appears that grompp, gtraj, and g_dist report the same value. Please also report the value that you get from your pullx.xvg file that you get from mdrun, which I suspect will also be the same. The difference that you report is actually between the first

[gmx-users] Umbrella sampling question

Can you please let us know exactly how you got the two values that you find to be different (but expected to be the same)? i.e. post your full g_dist command and explain how you observed the value in the output from mdrun. One frame should be enough for now (as long as you are sure -- and can pr

[gmx-users] Re: Setting up a complex membrane simulation

The simple answer is yes, you could make Lipid_A-box.gro larger in the bilayer plane. That probably won`t address the underlying problem though. As far as I know, genbox doesn't take periodicity into account. That means that with larger species, such as lipid A you are going to need to start wit

[gmx-users] How to avoid dumping trr file?

By dumping, I presume you mean writing it to disk during mdrun. set this in your .mdp file: nstxout = 0 nstvout = 0 nstfout = 0 And, while you are at it: nstlog = 0 Chris. -- original message -- Sometimes I do not need to dump the .trr file, which is really big. I am wondering if I can avoi

[gmx-users] Problem building Gromacs-4.5.5 on BlueGene/Q

Dear Dejun: I don't know why --enable-bluegene gives you problems or what it is supposed to do. Was the BGQ even available when gromacs 4.5.5 came out? I doubt it. In any event, here is how my colleague successfully ran configure: ./configure \ --build=ppc64 \ --prefix=${HOME}/exec/gro

[gmx-users] simulated annealing

your tau_t is 1 ps and you want to increase the temperature by 300 K in 10 ps. I doubt that this is possible. Try heating over a longer period of time. The longer the period, the closer you will get to your target temperature. Why do you need to do the heating over 10 ps? Also, when using any de

[gmx-users] Setting up a complex membrane simulation

Whatever method you use to set up your system, and be it atomistic or coarse-grained, I suggest that you build at least 2 such systems independently and run them all for the same amount of time. Looking at convergence from the same starting structure with different initial velocities is not nea

[gmx-users] regarding converge of system

RMSD of what? Probably you mean RMSD from the starting (or crystal) structure. First, consider that your profile of RMSD vs. crystal structure levels off at 0.4 nm with increasing simulation time. Consider how many possible conformations are 0.4 nm RMSD away from the crystal structure. A stable

[gmx-users] g_rdf

Dear Ali: I don't think that you are re-posting the same question often enough. Perhaps you should repost more often? 4 identical posts in 5 hours might not be enough to get a reply Seriously though, we all saw your message. Chris. -- original message(s) -- I have a system that conta

[gmx-users] Freeze group atoms changing position

makes sense. -- original message -- On 10/31/12 4:21 PM, Christopher Neale wrote: > Well, I thought that it would work for for freeze groups, and that is what I > intended to say. I've used freeze groups > before, but don't have tonnes of experience with them. The gromacs

[gmx-users] Freeze group atoms changing position

t 31, 2012 at 3:22 PM, Christopher Neale < chris.neale at mail.utoronto.ca> wrote: > No need to rename... just make an .ndx group. > > -- original message -- > > As I understand it, position restraints for an atom are set in the topology > file and applied to that atom in

[gmx-users] Freeze group atoms changing position

No need to rename... just make an .ndx group. -- original message -- As I understand it, position restraints for an atom are set in the topology file and applied to that atom in each of that species. In order to restrain some but not all of the water I'd have to copy the topology of my water mode

[gmx-users] What exactly is the artifact caused by setting refcoord_scaling=no with position restraint

I've asked the same question myself and would also like to know. That said, there seems to be no issue if you set refcoord_scaling=com. According to the manual, this does not give artefacts (whatever they are) and also does not change your restraint positions (as refcoord_scaling=all does). Sor

[gmx-users] time-block analysis

Leila, I provided 2 good references to answer your question earlier. If you can't be bothered to read about it, then the answer is yes, it is a good method. Looking at your other questions, I think that it is time for you to look at those references and learn more about block averaging and conve

[gmx-users] Re, density

Dear Ali: I am not sure what ecenter is, it looks like it might be the position to which the user wants to set the center? In any event, it doesn't mater for this modification. I did not write the center_x() function, it is a standard part of gmx_trjconv.c What I did was to copy center_x() to

[gmx-users] time-block analysis

Technically, in order to show that your simulation has reached complete convergence, you would need to show that every type of data has converged. Obviously nobody does this. You should start with looking at the convergence of any data type that you analyze in any other way. i.e. if you show a h

[gmx-users] Error during CNP simulation

You show different atoms before and after minimization so this is not proof of movement. I often resize my box by changing the value at the end of the file and have never had any problem with it. Of course, you do need to be careful with this and everything you do. Chris. -- original message

[gmx-users] Holes in the solvent!

In addition to the comments of Dallas Warren, which seems quite possible and should be checked, are you sure that you are seeing real holes and not just salt crystals that look like holes when you render only the waters with VMD? I have found that, at NaCL concentrations above 1 M, lipid bilaye

[gmx-users] time-block analysis

Dear Leila: I presume that "time-block analysis" is the same as block averaging, but it is impossible to be sure without more context. I suggest that you find the person who suggested that you do "time-block analysis" and ask them. Very generally, you will need to do your own scripting to do b

[gmx-users] g_density

Dear Ali: I assure you that all relevant information has been provided. As I said, it's not simple. If it is beyond your abilities then perhaps you should find a local collaborator. These days, many computational consortia have computational specialists who can help you with your scripting and

[gmx-users] Error during CNP simulation

Sorry Bharath, I simply can not believe that a macromolecule drifted 3 nm during energy minimization. What happened to the intervening solvent? I think that you have some problem with your technique here. Why did you use 120 constraints? Is this for bonds within the CNP? You need to do 2 things

[gmx-users] strange RMSD output

Try looking at the RMSD after fitting only the the backbone that is not in this variable loop. Since you are fitting to the whole protein, and your entire protein group is larger than your loop, your result does not surprise me. I would suggest: a) Do the fitting based on the backbone but excl

[gmx-users] Error during CNP simulation

I presume that your 7.5 nm -> 15 nm resizing refers to the Cartesian dimension that lies along the bilayer normal? Also, are you sure that the nanoparticle drifts significantly closer to the bilayer "during minimization", as you stated? That sounds unlikely. Perhaps this drift occurred during M

[gmx-users] g_rms problem

see, the rmsd of loop region is smaller than the backbone which I think it should be reversed... thank you very much. On 10/28/2012 05:03 PM, Christopher Neale wrote: > First, please let me complain that you did not run those 2 commands and post > the full output with the line on whic

[gmx-users] g_rms problem

First, please let me complain that you did not run those 2 commands and post the full output with the line on which you entered the command (for each one). Each command is expected to give you 10 lines of output, but you posted a single group of 12 lines. That seems like unlikely output and just

[gmx-users] g_rms problem

How many atoms are in each .pdb file? for i in $(ls *pdb); do grep ^ATOM $i|wc -l; done |sort -n |head for i in $(ls *pdb); do grep ^ATOM $i|wc -l; done |sort -n |tail Chris. -- original message -- I've 1000 separate pdb files generated by other Rosetta and I would like to calculate the RMS

[gmx-users] problem with g_density

All versions of g_density suffer from the same problem. It is not precisely a bug, since it works perfectly if you do constant volume simulations (presuming that trjconv -center works properly, which it does not in any version of gromacs) or if you properly process your trajectory prior to runni

[gmx-users] possible problem with gpc-f106n004

Dear SciNet: I have resubmitted, just letting you know. Thank you, Chris. starting mdrun 'title' 10 steps, 200.0 ps (continuing from step 101920720, 203841.4 ps). [[3105,1],27][../../../../../ompi/mca/btl/openib/btl_openib_component.c:3238:handle_wc] from gpc-f106n004 to: gpc-f106n0

[gmx-users] problem with g_density -center

The solution that I have posted with modified trjconv -center gives the correct values. However, you should always check such things because at the end of the day it is your name on the paper so you are the one responsible. If you want to reproduce a previous result, just contact them to find ou

[gmx-users] problem with g_density -center

Sorry Ali, I can't do your work for you. If this is way over your head, then either forget it, find a colleague to help you, or spend some time learning bash and gromacs. I'n not commenting on your approach, but if you modified your .gro then you need a new .top file. You can create one. Chris.

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