[gmx-users] umbrella sampling

2011-10-28 Thread chris . neale
You need to evaluate convergence yourself for any simulation. I suggest doing the whole thing twice (or more) with different starting conformations. Also, look at the PMF from block averaging (generate one PMF from the 0-2 ns data, another from the 2-4 ns data, and so on) and see if there

[gmx-users] Mismatching in Bergers DMPC bilayer lipid topology

2011-10-31 Thread chris . neale
Dear James: Next time, please specify exactly what you did in enough detail for somebody else to reproduce it, much as in a manuscript. e.g. there is no dmpc.gro in that website. I can guess what you did, but that is not ideal. I took a look at the files that I suppose you used and the

[gmx-users] umbrella sampling convergence

2011-11-01 Thread chris . neale
The criteria are the same for any type of simulation. Generally, you must show that, as far as you can tell, the values that you derive are not going to change if you run the simulation a lot longer. Different quantities converge at different rates, so ideally you should check them all

[gmx-users] source of opls Mg2+ parameters?

2011-11-02 Thread chris . neale
Dear users: does anybody know where the OPLS magnesium parameters are from? As far as I can tell, they are not in Jorgensen 1996 or Kaminski 2001, In spite of the fact that many simulation studies reference these papers for their magnesium opls parameters. In fact, I do not think that

[gmx-users] source of opls Mg2+ parameters?

2011-11-03 Thread chris . neale
Thank you Tom! Aqvist_A12 = sqrt(gromacs_C12*10^12/4.184) Aqvist_A6 = sqrt(gromacs_C6*10^6/4.184) (equation verified based on the SPC water oxygen parameters, also listed in Aqvist). This reference (Aqvist, J (1990) J. Phys. Chem., 94 (21), pp 8021?8024) should probably be noted somewhere

[gmx-users] umbrella sampling with pull=constraint

2011-11-07 Thread chris . neale
Dear Vijay: Can you please provide evidence for your claim that the harmonic potential is not applied properly, since you may decide to use pull=umbrella once you have set that up correctly. Importantly, movement out of the unit-cell is not a problem, as discussed a lot on this list.

[gmx-users] lipid bilayer and umbrella sampling

2011-11-07 Thread Chris Neale
If you add position restraints to your DPPC molecules, then you are changing your effective order parameter. The PMF for the solute along the normal to a restrained bilayer will have a different shape than a PMF for the solute along the normal to an urestrained bilayer. Whether or not this is

[gmx-users] Charged wall

2011-11-11 Thread chris . neale
You could create an atomistic charged wall by placing atoms in a plane or grid and using position restraints or freeze groups to keep them in place. You could them use the pull code to restrain part of the protein relative to an atom(s) in this atomistic wall. You could obtain your desired

[gmx-users] calculating the pmf in constrained force simulations

2011-11-26 Thread chris . neale
Do you mean that you do constrained position simulations and want to know how to process the force? If so, read about thermodynamic integration (TI). I mostly work with US and position restraints, but for absolute constraints I believe that you should take the average force at each

[gmx-users] to gro or not to gro

2011-11-26 Thread chris . neale
It's more useful if you provide more information. What was the .pdb file (can I download it from the pdb databank?) was there water? what version of gromacs? was it compiled in double or single precision? what were your mdp parameters? -- original message -- There is something not quite

[gmx-users] diffusion of the water at the micelle surface

2011-11-26 Thread chris . neale
When people do this for lipid bilayers, they compute depth-dependent diffusion profiles (often diffusion is computed separately for lateral diffusion and diffusion along the bilayer normal). Sounds like you might do something similar. I doubt that the standard gromacs tools will do this

[gmx-users] to gro or not to gro

2011-11-26 Thread chris . neale
There is rounding because of angstroms vs nanometers and both files maintain 3 decimal places (see below). The intention of pdb2gmx is not to get a .gro , but to get a .top or .itp file. I see your point, but I don't think it matters. If you really need that precision, then I'd think

[gmx-users] to gro or not to gro

2011-11-26 Thread chris . neale
1. why repeat the calculations? If you're talking about simulations then there is no need to repeat them due to this. You will get different answers with the same starting coordinates if you simply change the initial velocities. If you're talking about instantaneous energy calculations

[gmx-users] diffusion of the water at the micelle surface

2011-11-27 Thread chris . neale
Well, the positive way of looking at this is that it appears that nobody has ever done it before. If somebody has done it (in charmm for instance) then you might be able to convert the format of your .xtc and use their tools to analyze it. Good luck, Chris. -- original message -- Thank

[gmx-users] compiling with the PGI compiler

2011-11-30 Thread Chris Neale
I am using a new cluster of Xeons and, to get the most efficient compilation, I have compiled gromacs-4.5.4 separately with the intel, pathscale, and pgi compilers. With the pgi compiler, I am most concerned about this floating point overflow warning: ... [ 19%] Building C object

[gmx-users] Failed to lock .log. Already running simulation?

2011-12-01 Thread chris . neale
Dear Users: I have 50 simulations that are all the same, except with different random seeds for velocities. All were running fine for 24 hours. I canceled the running jobs and resubmitted them as part of beta testing a new cluster. All 50 started. I then canceled one of these jobs soon

[gmx-users] Half double pair list method in GROMACS [update]

2011-12-02 Thread Chris Neale
What you have done seems alright. I didn't look closely enough to be sure though. One of the good things about this method is that you can easily test it yourself. To do this, create two different .gro files, one containing the atoms from one ff and the other containing the other atoms. For

[gmx-users] intel grompp with pathscale mdrun

2011-12-06 Thread Chris Neale
Dear users: can I use a .tpr file created with an intel icc compilation of grompp and then do mdrun under a pathscale compilation of mdrun ? (same version of gromacs) I'm wondering if there would be some strange behaviour. It seems like it should be ok, but I wanted to be sure. I ask

[gmx-users] intel grompp with pathscale mdrun

2011-12-06 Thread chris . neale
= 3.467 ns/day pgi 11.8 = 3.092 ns/day pgi 11.8 with -tp istanbul -fast = 3.156 ns/day Again, thank you, Chris. -- original message -- As far as compilation hanging...maybe hand-compile that .o with less aggressive optimization flags, then try make again? MZ On Tue, Dec 6, 2011 at 2:20 PM, Chris

[gmx-users] Announcement: Large biomolecule benchmark report

2012-03-16 Thread chris . neale
You should absolutely publish this. it would be of great interest. You can mitigate your chances of running into problems with the overview by sending a version of the manuscript to the developers of each software and asking them to provide a short paragraph, each of which you could

[gmx-users] crazy temperatures

2012-03-28 Thread chris . neale
I disagree. What one is generally trying to obtain with elevated temperatures is enhanced sampling, not temperature-dependent properties. I believe that even TIP4P-EW is not very good at getting the properties of water correct at 600 K, temperatures that are commonly used during replica

[gmx-users] Umbrella sampling along Radius of gyration

2012-03-29 Thread chris . neale
It is not clear to me how one would do this with MD. The only thing that I can think of doing in gromacs is to create a virtual particle that is placed at the center of the protein and then apply forces along the vector from this virtual atom to each of the Ca atoms. You would need to

[gmx-users] Not able to continue with Equilibration

2012-03-29 Thread chris . neale
I didn't follow this whole thread, but I sometimes need to turn off all constraints when doing minimization. In fact, for that reason I entirely stopped ever using restraints during energy minimization. In extreem cases, I have had success also by forcing the water to be flexible with a

[gmx-users] How to compile the template.c when GMX is builded with cmake

2012-04-02 Thread chris . neale
Dear Users: I was previously able to compile template.c after I compiled gromacs with autoconf. I was unable to compile templae.c, however, I used cmake to compile gromacs. This is from gromacs-4.5.4. I tried cmake . in the template directory with no success: cmake .gpc-f102n084-$ cmake .

[gmx-users] on the Umbrella Sampling on-line tutorial

2012-04-02 Thread chris . neale
Dear Acoot: I'll reply to general topics, not to the tutorial in particular. If the opening is not large enough to allow the peptide to exit, then the surrounding protein will need to change its conformation to permit unbinding. This can happen, but you need (a) to have sufficiently long

[gmx-users] further discussion on the mdrun -append function

2012-04-05 Thread chris . neale
Dear Acoot: You should be able to answer this one yourself. Moreover, you are doing yourself a disservice by relying on the mailing list to do your work for you because you will eventually need to learn how to find answers to these things on your own. Please remember the following: 1.

[gmx-users] Different results from identical tpr after MD

2012-04-05 Thread chris . neale
Dear Acoot: The idea of convergence is this: start a large number of simulations from different conformations, analyze some quantity over time in each simulation, and when the deviation of the average value of that quantity from each separate simulation is less than the time-variance

[gmx-users] pull code with defined negative relative displacements

2009-11-14 Thread chris . neale
Hello, I am re-running some of our gromacs 3 simulations using gromacs 4, and as far as I can tell the gromacs 4 pull code, while very nicely enhanced from gromacs 3, has also lost some functionality. I am calculating the PMF of a peptide across a bilayer and, to simplify the issue, what I

[gmx-users] mdrun

2009-11-14 Thread chris . neale
Run some more energy minimization (EM). Make sure that you have constraints=none during EM (or I believe that you could also increase the LINCS/SHAKE iterations to the appropriate number). Also, while some people disagree in principle with me here, I also find in practice that a

[gmx-users] About rotational restraint

2009-11-14 Thread chris . neale
I haven't done it myself, but both of these methods appear as if they could be implemented out of the box in gromacs. On the use of orientational restraints and symmetry corrections in alchemical free energy calculations. Mobley DL, Chodera JD, Dill KA.

[gmx-users] pull code with defined negative relative displacements

2009-11-14 Thread chris . neale
Hi Justin, (comment to Berk below) thanks for pointing out the g_wham problem. I am personally ok here as I use a non-gromacs wham program. Hi Berk, unless I misunderstood, your suggestion does not yield the gromacs 3 behaviour that I am trying to reproduce with gromacs 4. If I simply

[gmx-users] pull code with defined negative relative displacements

2009-11-15 Thread chris . neale
Hi Berk, I am aware that pull_init=4.75 should pull to 4.75, not 1.0. I was mixing results from my simulations as I was discussing, sorry. Please allow me to restate the issue: If I am indeed pulling to 4.75 below group 0, then why is the force positive when group 1 has a displacement of

[gmx-users] pull code with defined negative relative displacements

2009-11-15 Thread chris . neale
I only now noticed Justin mail on g_wham. You can probably also use pull_geometry=distance and pull_init=1, if you starting structure has group1 close to 1 nm below group 0. Agreed, although this will not work when the force constant is not strong enough to inhibit any sampling 0 -- wherein

[gmx-users] pull code with defined negative relative displacements

2009-11-15 Thread chris . neale
Hi Berk, I do not mean the box 0, and I am aware about the pull distance needing to be less than half of the smallest box length. Please allow me describe a bit more rigorously what I need to avoid. I will use an example that is totally fictitious, but is designed to emphasize the

[gmx-users] PULLING

2009-11-15 Thread chris . neale
First let me mention that I only scanned the mammoth manuscript snippet. Nevertheless, I'll try to address your questions. 1. You are physically able to use spc in place of tip3p. Whether or not that is a good idea is up to you to decide. Read the literature including the spc, tip3p, and

[gmx-users] ull code with defined negative relative displacements

2009-11-15 Thread chris . neale
Thank you very much Berk, I'm not trying to be argumentative for arguments sake, but I just can't see how exactly one would make pull_geometry=direction work in this way. Although I think that I have shown the evidence for this in my posts, if I am wrong here then clearly I misunderstand

[gmx-users] PULLING

2009-11-16 Thread chris . neale
Sorry for so disordered questions... 3. use the pull code. I don't know exactly what you want to do here...perhaps harmonically restrain the distance between the two mentioned groups to some specified value? No need to rename the water, just make an index group. The problem is that I don't know

[gmx-users] pull code with defined negative relative displacements

2009-11-18 Thread Chris Neale
Hi Berk, I have done the tests and you are entirely correct. I have one further question: If I simply want to pull to a relative displacement of -1.0 nm, is there any reason to prefer one of these methods, or are they just overlapping implementations of different methods that also have

[gmx-users] trjconv -pbc cluster with rhombic dodecahedron box

2009-11-30 Thread chris . neale
Hi Daniel, I think you still need to read and attempt what has already been suggested. To be more explicit: trjconv -f a.xtc -o a_cluster.gro -e 0.001 -pbc cluster grompp -f a.mdp -c a_cluster.gro -o a_cluster.tpr trjconv -f a.xtc -o a_cluster.xtc -s a_cluster.tpr -pbc nojump from:

[gmx-users] trjconv -pbc cluster with rhombic dodecahedron box

2009-12-01 Thread chris . neale
Hi Daniel, 1a. I am confused about what is your vesicle. Is it everything that you are showing in these images? Or perhaps it is only the cyan thing that I can see sliced through in: http://img109.imageshack.us/img109/8227/trajenddat.jpg 1b. I suspect that the cyan ring encircled by

[gmx-users] trjconv -pbc cluster with rhombic dodecahedron box

2009-12-01 Thread chris . neale
There is no problem with the rhombic dodecahedron in and of itself. Note that editconf -d does not actually yield the -d that you ask it to and that it errs on different sides of your request for different box types. To prove this to yourself, run your starting structure through editconf

[gmx-users] PMF calculation using g_wham using different simulation boxes

2009-12-02 Thread chris . neale
Hi Li, In my opiniun, what you propose is acceptable, but not rigorous, and you will need to prove that there are no unexpected artifacts of changing box size. For example, you should definitely run a couple of your small box systems as larger boxes as well and show that you get the same

[gmx-users] any chance to write avoid writing out trr but only xtc file ?

2009-12-02 Thread chris . neale
We have the same desire on a large cluster in order to reduce the number of file operations overall. In addition to Xavier's suggestion, you can also write your .trr to memory: mdrun -deffnm xx -t /dev/shm/xx.trr or to the local disk: mdrun -deffnm xx -t ${TMPDIR}/xx.trr if those exist and

[gmx-users] .cpt file not used for mdrun input in the absence of the -cpi flag

2009-12-02 Thread chris . neale
Hello, I have just realized that an existing checkpoint file will not be used as input to mdrun when its name is supplied via -deffnm but not directly via -cpi. I suppose that this makes sense for backward compatibility, and the mdrun -h -cpi state.cpt Input, Opt. Checkpoint file

[gmx-users] any chance to write avoid writing out trr but only xtc file ?

2009-12-02 Thread chris . neale
Thanks Berk, I agree that a single file open action is not going to cause a lot of system activity. We're simply trying to cut down wherever possible as this is a large shared cluster where the activity of many users distributed amongst 30K cores is overwhelming the GPFS. We have been

[gmx-users] Pressure annealing in Gromacs?

2009-12-02 Thread chris . neale
Sounds like a phase change. If that is the case, 10 ns is likely not enough to expect equilibration considering that bilayers can take 50ns (or even substantially longer) to equilibrate the area per lipid after a phase change. None of this is to contradict your intuition about a

[gmx-users] PMF calculation using g_wham using different simulation boxes

2009-12-02 Thread chris . neale
Sorry, I don't use gromacs g_wham so I can't help you on the specifics there. I don't know if the -zprof0 does anything special, but you know that your PMF can be arbitrarily translated as dG is unknown to an additive constant, right? ## assume rx coord in first column and dG in second

[gmx-users] program to look at the coordination number

2009-12-02 Thread chris . neale
You did not state clearly what you want to do. In many cases you could simply calculate the RDF using g_rdf and integrate to the first minimum. If that doesn't suit you, here's another idea: 1) g_rdf - locate the first minimum 2) g_dist -dist to print all the atoms in group 2 that are closer

[gmx-users] spatial distribution function (SDF)

2009-12-03 Thread chris . neale
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?

[gmx-users] some questions about umbrella sampling

2009-12-10 Thread chris . neale
I am doing umbrella sampling to calculate energy profile of an drug passing through a ion channel by GROMACS3.3. why not gmx 4? In order to get right result, I need to choose a reasonable force constant in my simulation, right? I know that, a reasonable force constant should produce

[gmx-users] where is the gromacs 4.0.6/7 revision list?

2009-12-11 Thread chris . neale
Hello, I am very interested to know exactly what has changed between gromacs 4.0.5 and 4.0.6/7. I understand that the test set is no longer useful for gmx-4 (see quote below) and I'm not strongly motivated to update my gromacs version when I don't know what bugs will be fixed and there

[gmx-users] where is the gromacs 4.0.6/7 revision list?

2009-12-12 Thread chris . neale
Thanks for taking the time Mark, this is quite useful. Especially Bug 354: switching from Berendsen to V-rescale doesn't work if -nosum is used for those of us who don't follow the list every day. -- original messagwe -- I started a 4.0.7 revisions list there and noted the issues that came

[gmx-users] where is the gromacs 4.0.6/7 revision list?

2009-12-12 Thread chris . neale
Thanks again Mark, are you able to provide a bug number for Fixed bug with pull groups using weights in parallel so that I can figure out exactly what the problem was? Separately, it seems like a decent idea to automate the production of this list and its update on the website whenever a

[gmx-users] Check for bad contacts and/or reduce the timestep

2009-12-16 Thread chris . neale
I believe that Justin was suggesting that you move in the opposite direction than to delete some waters. The number density for water should be about 32.5 waters per cubic nanometer, meaning that you should have nearly 1E6 water molecules in a cubic box with sides of 31 nm, and 1095 water

[gmx-users] Frequency confout is updated

2009-12-16 Thread chris . neale
You could also have a script that you optimize for your specific system that knows the number of frames in the xtc based on the file size and then trjconv -dump when your .xtc-polling script sees that it has been updated? Your visualization program could then update based on the output

[gmx-users] LIE precision and accuracy

2009-12-17 Thread chris . neale
In spite of the fact that I have never used g_lie, I have used a variety of different techniques to calculate binding free energies, and I would be astounded if it was possible to get the precision that you desire with only 1 ns of sampling per state. Are you sure that the reported

[gmx-users] reference for make_edi -linacc

2009-12-18 Thread chris . neale
Hello, does anybody have a reference for the -linacc method applied by make_edi/mdrun? I have checked the references mentioned in make_edi -h as well as the manual, but didn't find anything that matches -linacc exactly. For example, gromacs suggests that entire MD steps will be accepted

[gmx-users] reference for make_edi -linacc

2009-12-18 Thread chris . neale
Than you Ran, this looks good. The method is basically the same with the exception that Daidone et al. utilize a target structure as opposed to a target eigenvector, although the difference here is probably semantic. I greatly appreciate it, Chris. -- original message -- Hi Chris, Maybe

[gmx-users] pdb2gmx -merge non interactive

2009-12-18 Thread chris . neale
Can't you just do one of these: echo 5 | pdb2gmx -f a.gro or pdb2gmx -f a.gro EOF 5 EOF --original message-- Hi List, is it possible to have the -merge option in pdb2gmx set to non-interactive? I need to merge 8 copies of a protein into one definition (.top) because if i don't do that all

[gmx-users] pdb2gmx -merge non interactive

2009-12-18 Thread chris . neale
What exactly did you try? Something like this? pdb2gmx -f a.gro EOF 5 y EOF I have not done -merge myself, but I often pass in multiple 'command-line' arguments in a scripts, although it is necessary to run it through on the command line once to see what the order of arguments should be.

[gmx-users] exclusive list of matching searches on the gmx-users list

2009-12-18 Thread chris . neale
Hello, does anybody know how to get an exclusive list of matching searches while searching the gromacs mailing list using the new search tool? I have tried: essential dynamics Address not mapped essential dynamics and Address not mapped essential dynamics AND Address not mapped essential

[gmx-users] essential dynamics mdrun with SD integrator yields segmentation fault

2009-12-18 Thread chris . neale
Hello, In my hands, mdrun throws a segfault when passing the -ei flag to mdrun and utilizing the sd integrator. I'll admit that I have only tried this with a single system. Nevertheless, using -linacc vs. -linfix makes no difference, neither does moving to constraints=none or parallel

[gmx-users] multiple eigenvectors with -linfix and the application of eigenvalues

2009-12-19 Thread chris . neale
Hello, When utilizing more than one eigenvector in make_edi -linfix, are the eigenvector linearly combined with their eigenvalues as coefficients, or does this combination occur in the absence of eigenvalues? Thank you, Chris. -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] multiple eigenvectors with -linfix and the application of eigenvalues

2009-12-21 Thread chris . neale
Thank you Carsten for this information and for the sd/edi fix. This actually makes a bunch of sense. I can effect the eigenvalues with -linfix -linstep, and I see now that eigenvalues can not be sensibly combined with -linacc in in its current incarnation. Thank you, Chris. -- original

[gmx-users] make_edi fails with multiple eigenvectors for -linfix and -linacc

2009-12-23 Thread chris . neale
Hello, I am having trouble getting make_edi -linfix to work with multiple eigenvectors. This works for a single EV: $ echo 3 | make_edi -s ../../SETUP/makeTPR/edi.tpr -f ../../SETUP/makeEDI/eigenvec.trr -o testpositive.edi -linfix 1 -linstep 0.0001 -outfrq 50 And throws an error for:

[gmx-users] Depth of penetration of DMPC lipid bilayer. How?

2009-12-23 Thread chris . neale
Be careful when you draw conclusions from your results though. I suggest that you start two simulations from different coordinates and look at their convergence. In my hands, this type of thing can take 1 us to converge, and that's without any major conformational changes in the

[gmx-users] fix a group in truncated octahedron

2009-12-27 Thread chris . neale
Hi Wende, please do not double post. If you are unsure if your post got through, you can easily see the list at http://lists.gromacs.org/pipermail/gmx-users/2009-December/date.html. You did not put units beside 40, so I suppose that you mean 40 A, whereas gromacs uses nm. 1. Make a box

[gmx-users] trjconv -pbc: how to keep all parts of the system clustered together in PDB?

2009-12-28 Thread chris . neale
Search: trjconv pbc cluster on the gromacs mailing list and take a look at the first hit. Basically, you need to find a frame that *does* work with -pbc cluster and then make a new .tpr based on the clustered .gro and then run trjconv -pbc mol. Just ensure that this frame is as close to the

[gmx-users] pdb file for ammonia

2009-12-31 Thread chris . neale
Hi Nisha, Hetero-Atom Navi is a collection of heteroatoms culled from the PDB. http://hetpdbnavi.nagahama-i-bio.ac.jp/index.php?mode=0 However, having only one heavy-atom, ammonia is unlikely to be usefully extracted from this resource for use in atomistic MD. You can easily make it

[gmx-users] angle_restraints_z and -ddcheck

2010-01-02 Thread chris . neale
Hello, I have just started working with the [ angle_restraints_z ] portion of the code. My initial tests indicate that it works in my system. However, in some cases I am getting a fatal error that a pair interaction is too far apart to be calculated within domain decomposition. Although

[gmx-users] particle decomposition requires preliminary trjconv -pbc mol input

2010-01-03 Thread chris . neale
Hello, I recently used mdrun -pd while attempting to solve my problems with angle_restraints_z (http://lists.gromacs.org/pipermail/gmx-users/2010-January/047785.html) since I discovered that -noddcheck is not a valid solution to the missing interactions problems with angle restraints.

[gmx-users] angle_restraints_z and -ddcheck

2010-01-05 Thread chris . neale
I have determined that the proper solution here is to use particle decomposition. -noddcheck simply delays the inevetable fatal LINCS error. Nevertheless, mdrun -pd requires that one maintains whole molecules in the starting conformation:

[gmx-users] Incomplete frame,while running trjconv .....

2010-01-05 Thread chris . neale
Your disk was full and the .xtc file could not be completely written, therefore you have an incomplete frame. I think that you have answered your own question here. If I was you, I would trjconv -e to get the full trajectory minus the last incomplete frame for a good .xtc file. There are

[gmx-users] Error during minimization

2010-01-05 Thread Chris Neale
Hi Nisha, you say And it runs minimization with bad contact errors, but I don't see any indication of that error message here. Is it perhaps that your EM exits early and then your MD throws an error? In any event, please post complete error information as output by gromacs. Chris. --

[gmx-users] low concentration simulation ?

2010-01-05 Thread Chris Neale
Mark already answered this: http://lists.gromacs.org/pipermail/gmx-users/2010-January/047825.html --original message -- HI I am simulating the protein + ligand + water molecules system. In the experimental work, the concentration of ligand is pretty low, say under 20 mM (avearge 18 ligands

[gmx-users] particle decomposition requires preliminary trjconv -pbc mol input

2010-01-07 Thread chris . neale
future users experiencing this problem can follow this thread at: http://bugzilla.gromacs.org/show_bug.cgi?id=383 -- original message -- Hi, Can you file a bugzilla and attach the tpr file? Thanks, Berk Date: Tue, 5 Jan 2010 10:49:46 -0500 From: chris.neale at utoronto.ca To: gmx-users at

[gmx-users] PR for CG lipid and CG protein

2010-01-09 Thread chris . neale
Dear Sunny, I replied a while ago, but it seems to have not made it to the list. When using inflategro with gromacs3, you can run cycles like this: 1. inflategro.pl 2. mdrun (EM) 3. goto 1 When running with gromacs4, however, you must run cycles like this: 1. inflategro.pl 2. mdrun (EM) 3.

[gmx-users] PR for CG lipid and CG protein

2010-01-09 Thread chris . neale
Hi Justin, I just double checked and certainly the confout.gro from my EM run in parallel with domain decomposition in mdrun is broken over periodic boundaries. I'm running gromacs-4.0.5 on a nehalem under openmpi. Here is my .mdp file gpc-f101n084-$ cat em_pos.mdp define=-DPOSRES_INDO

[gmx-users] confout.gro contains PBC-broken molecules after EM in parallel with domain decomposition

2010-01-09 Thread chris . neale
Hi Justin, I can confirm that I see that code snippet in my md.c code, although my tests indicate that this is not the end of the story. I have now taken the output .gro, ran it through trjconv -pbc mol and then ran mdrun again under a variety of conditions: 1. EM(steep) mdrun_mpi

[gmx-users] particle decomposition requires preliminary trjconv -pbc mol input

2010-01-09 Thread chris . neale
Thanks Berk, increasing -rdd from 1.0 to 2.5 has solved my problem. Note that the actual distance between the two atoms in the angle restraint never exceeds 0.9 nm, although this is a rather complex set of virtual atoms based on the positions of other virtual atoms, each virtual atom in

[gmx-users] confout.gro contains PBC-broken molecules after EM in parallel with domain decomposition

2010-01-09 Thread chris . neale
Good idea Justin. I have posted as bug 386. -- original message -- On 1/9/10 1:44 PM, chris.neale at utoronto.ca wrote: Hi Justin, I can confirm that I see that code snippet in my md.c code, although my tests indicate that this is not the end of the story. I have now taken the output .gro,

[gmx-users] InflateGRO and trimer simulation

2010-01-10 Thread chris . neale
Try the doughnut mode in the newest version of the program -- it's meant for exactly this situation. http://www.csb.bit.uni-bonn.de/inflategro.html -- original message -- Hello Gromacs Users, I would like to run a simulation of a trimer in a DPPC membrane. I really like the elegant solution

[gmx-users] Error while pulling a settled tip4p water molecule

2010-01-14 Thread chris . neale
I have done a similar thing in the past (without using the pull code), renaming the crystal waters around the protein so that they were easier to track. I eventually figured out that it was necessary for me to place the waters sequentially in the .top file. e.g: ; This is OK Protein 1

[gmx-users] SImulation error grompp

2010-01-14 Thread chris . neale
Probably you removed lipids from the gro but not from the top (which you need to do as well). Find a lipid atom name that occurs only once per molecule (In non-united atom lipids I use P8) grep P8 my.gro |wc -l This will tell you how many lipids should appear in your top file. Chris. --

[gmx-users] Ammonia in Water

2010-01-15 Thread chris . neale
First, I doubt that you want a molecule with a partial charge. Second, just because the bonds, angles, and LJ parameters will be generated doesn't mean they will be correct. What are the N-H bond lengths of ammonia? Are those the same as the ones that you are including here? Take a look at

[gmx-users] CHarmm and popc membrane

2010-01-15 Thread chris . neale
I think the notes from grompp are pretty clear. You need to redivide your charge groups so that they contain fewer atoms. You can do this in the .top or .itp file and you can find out how to do that in the manual. Feel free to post your original and charge-group-modified topologies back

[gmx-users] Scaling of Coordinates is Occurring - why?

2010-01-16 Thread chris . neale
From what I can find, it seems that you are correct to assume that frozen coordinates should not be scaled: http://lists.gromacs.org/pipermail/gmx-users/2002-July/002054.html and, from the online manual: freezegrps: Groups that are to be frozen (i.e. their X, Y, and/or Z position

[gmx-users] The size of the domain decomposition grid (1) does not match the number of nodes (8).

2010-01-16 Thread chris . neale
Hello, I have a run that was working fine under parallel mdrun -pd and when I then switched to domain decomposition I got: Fatal error: The size of the domain decomposition grid (1) does not match the number of nodes (8). The total number of nodes is 8 while running like this:

[gmx-users] CHarmm and popc membrane (response to Missing Residues are list ind pdb file)

2010-01-18 Thread chris . neale
Hi Stefan and Pär, I believe that the latest response had the wrong subject, so I am changing it back. Pär, two comments: First, does that option really exist? $ /scratch/cneale/GPC/exe/intel/gromacs-4.0.7/exec/bin/pdb2gmx -h z 21; cat z|grep nochargegrp|wc -l Second, I am not

[gmx-users] CHarmm and popc membrane

2010-01-18 Thread Chris Neale
That's why I said if you know what you're doing :) ok, fair enough. The name flag is listed as [no]chargegrp I still don't see it (see below), is this [no]chargegrp new in the cvs ? I'm pretty sure that you're not referring to [no]lys, etc. $

[gmx-users] Implicit Solvent

2010-01-21 Thread chris . neale
implicit solvent has apparently been implemented in the openMM modification of gromacs, although that is still in beta and is not to be trusted for production runs without doing your own testing. I have not tried it myself. You can obtain it here: https://simtk.org/home/openmm -- original

[gmx-users] fitting dihedral angle function parameters using gromacs

2010-01-23 Thread chris . neale
I have never done this myself. Nevertheless, I'm going to take a shot since you haven't got an answer yet. Dihedral parameters can be thought of as consistently developed fudge factors that are used to fine-tune a parameter set. The word consistent here implies that there is a method to

[gmx-users] CONSTRAINED SIMULATIONS

2010-01-24 Thread chris . neale
Please provide actual gromacs output and tell us where it is from. I know it's sad, but not all of us can recall what the gromacs 3.3.3 .pdo file format looked like. So please include a sufficiently large portion of the file to help us recall. If, on the other hand, these values that you

[gmx-users] strange empty space inside the system box

2010-01-24 Thread chris . neale
Sounds like a bubble. Do some NpT equilibration by adding pressure coupling. That's going to be difficult with your freeze groups though. Basically, you need to find a way to get the correct solution density between the graphite layers. -- original message -- Hi all, Is there anyone who

[gmx-users] simulation crash with GROMOS96 force field

2010-01-24 Thread chris . neale
1. Is your system is properly minimized 2. If you take the output from a 500 ps run with 0.25 fs timestep and start a 1 fs timestep run, is that new run stable? 3. What are atoms 62 and 80? **4. Why is there a 1-4 between atoms 62 and 80 if you have only water and a 42 atom solute? 5. What

[gmx-users] CONSTRAINED SIMULATIONS

2010-01-24 Thread chris . neale
Dear Giuseppe: I don't think your method of showing the change is very good since it introduces unnecessary variables (e.g. did you use the correct files for the second run). What I am looking for is raw -pd pull.pdo data from the first run. I found no such file in the body of the email

[gmx-users] CONSTRAINED SIMULATIONS

2010-01-24 Thread chris . neale
Dear Giuseppe: *** What I am looking for is raw -pd pull.pdo data from the first run. *** It looks like you did not define a name for -pd: mpiexec -n $NSLOTS mdrun_mpi -np 1 -v -s start_res.tpr -o output_res -c output_conf -pi pull.ppa -pn mdgrp1.ndx -po pullout -pdo pullout1 * so based on

[gmx-users] Re: simulation crash with GROMOS96 force field

2010-01-24 Thread chris . neale
1. Is your system is properly minimized Of course, it is, based on the energy values. Don't be so sure! Although since your 0.25 fs timestep -- 1 fs timestep transition crashes you are likely correct here. **4. Why is there a 1-4 between atoms 62 and 80 if you have only water and a 42

[gmx-users] CONSTRAINED SIMULATIONS

2010-01-24 Thread chris . neale
Dear Giuseppe: OK, those are the forces. They seem pretty huge and massively fluctuating, although I use umbrella sampling myself so this might be quite normal for constraint sampling (something for you to look into). The only thing that comes to mind is that your running up against a

[gmx-users] Re: simulation crash with GROMOS96 force field

2010-01-24 Thread chris . neale
Dear Vitaly: Justin raises the point well, so that should be addressed first. If, however, you still have problems then there's the only thing that I can think of: 1. put a single solute in a large vacuum box and use the sd integrator. Can you reproduce the problem? 2. Remove the

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