Re: [gmx-users] g_spatial: merging solvent ond solute:::need some distance

To help you, I need to see the exact commands that you used. Best is if you can put it all in a script, run the script to be sure that you see the problem, and then copy and paste the script back to this list. Failing that, copy and paste your commands and tell me what your command-line input

Re: [gmx-users] pull_geometry=direction

Try using pull_geometry = direction-periodic For more details, see http://bugzilla.gromacs.org/issues/1352 Chris. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Lalita Shaki

Re: [gmx-users] pull_geometry=direction

some literture about the effect of using the NVT ensemble or the NPT one? Is there any major difference between pull_geometry = direction-periodic and pull_geometry = direction? Thank you Lalita Message: 1 Date: Thu, 9 Jan 2014 16:32:27 + From: Christopher Neale chris.ne...@alum.utoronto.ca

Re: [gmx-users] REMD slow's down drastically

Presuming that you have indeed set up the number of processors correctly (should be running on a different number of cored for different number of replicas to do a fair test), could it be a thread pinning issue? I run on a Nehalem system with 8 cores/node but, because of the Nehalem

Re: [gmx-users] REMD slow's down drastically

down drastically On Feb 24, 2014 11:01 PM, Christopher Neale chris.ne...@alum.utoronto.ca wrote: Presuming that you have indeed set up the number of processors correctly (should be running on a different number of cored for different number of replicas to do a fair test), could it be a thread

Re: [gmx-users] md_pull code in umbrella sampling

It's not US if you have a non-zero pull-rate1 that gets applied during your simulation, although with your pull-geometry=distance I don't think that pull-rate is even used (therefore I think that part is technically correct, although your .mdp file is confusing on this issue). Careful that X

Re: [gmx-users] Out of Disk Space

It could be a quota issue (there is free space, but your group has used its entire allocation). Also, file systems often have limits not only on the total amount of space, but also on the total number of files that a group is allowed to create. Talk to your system administrator. There is likely

Re: [gmx-users] Assistance needed running gromacs 4.6.3 on Blue Gene/P

I've run gromacs v4.6.3 on BG/Q without problem and my colleagues have run older versions of gromacs on the BG/L also without problem. (No BG/P experience here, unfortunately). Still, it's worth having you post your job submission script for us to take a look at. Also, is it just gromacs

Re: [gmx-users] Assistance needed running gromacs 4.6.3 on Blue Gene/P

I have run into similar error messages running gromacs 4.6.2 on some new Xeon's. That cluster is having file system problems sporadically and I end up with jobs that die about 1% of the time with message like this: mdrun_mpi:21408 terminated with signal 6 at PC=38e02328a5 SP=7f534f467738.

Re: [gmx-users] PEG residue

My colleague and I have simulated atomistic polymers containing PEG. If the issue is just parameters, you can find them here: http://pubs.rsc.org/en/content/articlelanding/2010/sm/c001988g#!divAbstract From:

Re: [gmx-users] Unable to generate file.gro with gromacs.4.6.3-1

where do you learn this stuff ? ;) From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul jalem...@vt.edu Sent: 22 March 2014 21:50 To: gmx-us...@gromacs.org Subject: Re:

Re: [gmx-users] refcoord-scaling

Say you have a box with an x-side length of 3 nm and two atoms with x-dimension position restraints to: (a) x=1 nm, and (b) x=2 nm Then let the box shrink to 99% of its previous size due to pressure coupling. The following is my understanding of the locations to which the atoms will be

Re: [gmx-users] REMD, demux after 100 ns per replica

I have used demux.pl from gromacs 4.6.3 on files up to 1 us per replica simulated with gromacs 4.6.1. For my usage, the first column of both output .xvg files (replica_index.xvg and replica_temp.xvg) is fine up to 1 microsecond, then moves to scientific notation but, unfortunately, there are

Re: [gmx-users] pdb2gmx yielding (a couple of) -nan values for coordinates of built hydrogen atoms

-linear). Mark On Fri, Apr 18, 2014 at 4:47 AM, Christopher Neale chris.ne...@alum.utoronto.ca wrote: In most cases, I get what I expect when I execute the following command: echo -e 6\n1\n | pdb2gmx -f ${b}e.gro -o ${b}et.gro -p tmp.top -i ${b}_posre.itp -ter -ignh However, I have one input

Re: [gmx-users] REMD, demux after 100 ns per replica

Dear Andrea: I can't access your script now that posts have been removed from nabble. I have tried changing demux.pl line 70 from: $tstep = $log_line[6]; to: $tstep = 0.002 * $log_line[4]; where 0.002 is my timestep. Did you do this or something similar? Thank you,

Re: [gmx-users] REMD, demux after 100 ns per replica

. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Christopher Neale chris.ne...@alum.utoronto.ca Sent: 02 May 2014 14:28 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] REMD, demux after 100 ns per replica Dear

Re: [gmx-users] trjcat finds different spacing among trajectories

When you run gmxcheck on md_0_1.part0014.xtc and md_0_1.part0015.xtc separately, what start and end times do you get for each of the two files? From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on

Re: [gmx-users] quesion about MIC

I recall reading somewhere that MIC support is only native at this point. That is, you can run simulations entirely on MICs, but not hybrid CPU-MIC simulations. Don't recall where I read that and can't easily find it online. Chris. From:

Re: [gmx-users] translational dipole moment during the simulation

I can't help with the source code modification, and I am surprised that you actually need 5 fs resolution, but if you are simply having trouble with disk space, you could set up a loop inside your job script that (a) runs mdrun, (b) extracts velocities, (c) makes a copy of the raw output,

Re: [gmx-users] Secondary structure not visible after convertingfrom .gro to .pdb

I sometimes see this in VMD if the coordinates are truly awful (e.g, if the C-alpha atoms are way too far apart, then VMD does not recognize it as a proper backbone since no topology information is loaded and connectivity is inferred from distances). I also see this for some crystal structures

Re: [gmx-users] Secondary structure not visible after converting from .gro to .pdb

Sounds reasonable now. If 10 molecules are all listed as part of the same chain (PDB format) then maybe Pymol will stop rendering after the first chain. So either script changing the chain info or find some other way to have them listed as different chains in the .pdb or (perhaps) just use a

Re: [gmx-users] Possible trjconv malfunction?

You listed: echo 0|trjconv_mpi -f stn_wt_a_fit_1.xtc -s stn_wt_a_1.tpr -b 20002 -e 2 -o g96/stn_wt_a_1_0.g96 -novel And your -b value is less than your -e value, so you should not get any output, which is what happens. Try using -dump to extract a single frame. If you want, you can also

Re: [gmx-users] Possible trjconv malfunction?

as well to speed up trjconv! Best Wishes, Nathan On Thu, Jun 26, 2014 at 1:12 PM, Christopher Neale chris.ne...@alum.utoronto.ca wrote: You listed: echo 0|trjconv_mpi -f stn_wt_a_fit_1.xtc -s stn_wt_a_1.tpr -b 20002 -e 2 -o g96/stn_wt_a_1_0.g96 -novel And your -b value is less than your

[gmx-users] Is the discontinuity in type 2 improper dihedrals at 90 deg. or 180 deg. ?

Dear Users: In gromacs, the charmm27 force field uses type 2 (non-periodic) improper dihedrals to maintain planarity of peptide bonds. Type 2 dihedrals are described on page 70 of the 4.6.7 manual and page 80 of the 5.0.2 manual, which contain the line (identical text): Since the potential is

[gmx-users] Is the discontinuity in type 2 improper dihedrals at 90 deg. or 180 deg. ?

Dear Justin: Thank you for the insight. I had mistakenly thought that the combination of two overlapping impropers was what was inhibiting omega inversions. Obviously you are correct. Thank you, Chris. On 12/13/14 9:28 PM, Christopher Neale wrote: Dear Users: In gromacs, the charmm27

[gmx-users] how to decouple a solute (a) only from itself and not the solvent, and (b) leaving the LJ repulsive term unmodified

Dear Users: I'm trying to induce a protein to unfold and I'd like to use a free-energy-like lambda value to specifically weaken only the attractive part of the LJ interactions within the protein, while leaving LJ interaction between protein and water unmodified. Is there any way to do this in

Re: [gmx-users] how to decouple a solute (a) only from itself and not the solvent, and (b) leaving the LJ repulsive term unmodified

08:02 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] how to decouple a solute (a) only from itself and not the solvent, and (b) leaving the LJ repulsive term unmodified On 12/17/14 12:44 AM, Christopher Neale wrote: Dear Users: I'm trying to induce a protein to unfold and I'd like to use

Re: [gmx-users] How to change the multiplicity of a dihedral in FEP in Gromacs

Add two dihedrals with different multiplicities and phase one out while you phase one in ? From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of bipin singh bipinel...@gmail.com Sent: 18

Re: [gmx-users] Energy minimization problem in Choline Chloride+Urea mixture in Gromacs

Can you simulate a single molecule of choline in vacuum without it crashing? What about urea? From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Suman Das sumandas...@gmail.com Sent: 02

[gmx-users] tabulated non-bonded potentials with replica exchange (potentials that change with temperature)

Dear Users: I presume that I can use tabulated non-bonded potentials with replica exchange in gromacs 4.6.7. However, my question is whether it is possible to supply different tables for each of the different temperatures? My actual use involves the plumed plugin to do hamiltonian replica

Re: [gmx-users] make_ndx selection of backbone residues

Make a group of the or selections first, then run an and on group 4 and your new group. I don't exactly remember, but maybe you can do it in one step by simply putting the 4 at the end instead of the beginning. Chris. From:

Re: [gmx-users] Semiisotropic pressure coupling

Dear Justin: If you have time, can you please provide a link / reference for your comment that potential switching leads to errors in the charmm lipid force field? I tried a google search, but couldn't come up with anything specific. You mentioned noticeable artifacts, so I'm hoping that you

[gmx-users] g_cluster (gromos method) creates clusters with members having RMSD greater than the cutoff to the cluster middle

Dear Users: I have run g_cluster from gromacs 4.6.5 as follows: g_cluster -s my.tpr -f tmp.xtc -method gromos -nofit -o rmsd-clust_nofit.xpm -g cluster_nofit.log -sz clust-size_nofit.xvg -cl clusters_nofit.pdb -n index.ndx -cutoff 0.275 -wcl 10 -cl finally.xtc The top of cluster_nofit.log

Re: [gmx-users] Variable force constant in umbrella sampling

Dear Daniel: It is perfectly fine to use different force constants for different umbrellas. This is commonly done, for example, when you have a very sharp maximum in your PMF and you need to place a few umbrellas at and near this maximum with very strong force constants in order to get good

Re: [gmx-users] Fwd: how to calculate angles (molecules directions)

How does one compute the angle between a vector and a molecule? I think you need to define your goal more completely. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Maryam Kowsar

Re: [gmx-users] Fwd: how to calculate angles (molecules directions)

. I think I should try g_dipole. thank you very much! Cheers, --Maryam On Fri, Feb 13, 2015 at 8:42 AM, Christopher Neale chris.ne...@alum.utoronto.ca wrote: Dear Maryam: I don't know. If g_dipoles doesn't give you what you want (and I have no idea if it will), then g_traj -ox will give you

Re: [gmx-users] Fwd: how to calculate angles (molecules directions)

? thank you! On Fri, Feb 13, 2015 at 8:18 AM, Christopher Neale chris.ne...@alum.utoronto.ca wrote: How does one compute the angle between a vector and a molecule? I think you need to define your goal more completely. From: gromacs.org_gmx-users-boun

Re: [gmx-users] gromacs

(A) modify your .mdp to increase nsteps and then make a new .tpr, then run mdrun -cpi my.cpt files and use the new .tpr file. (B) use tpbconv to modify your original .tpr file and then rerun using mdrun -cpi (C) simply run as before (though you need -cpi option to mdrun since it is a restart)

Re: [gmx-users] Semiisotropic pressure coupling

Thanks guys, this is very useful. Chris. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul jalem...@vt.edu Sent: 13 February 2015 16:53 To: gmx-us...@gromacs.org Subject:

Re: [gmx-users] Fwd: Odd behavior in log files for two simulations with only different nstlog for Gromacs 5.0.4

Not sure about the differences, but focusing on what is similar: you're not getting anything close to the desired temperature (in one case half and in one case 3 times after only 10 integration steps). I suspect that there is something else going wrong. I've never combined the sd integrator

Re: [gmx-users] g_cluster (gromos method) creates clusters with members having RMSD greater than the cutoff to the cluster middle

Dear Users: I have sorted out the issue and filed a redmine: http://redmine.gromacs.org/issues/1688 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Christopher Neale chris.ne

[gmx-users] g_density appears broken in version 5

Dear membrane simulators: If you use g_density from gromacs versions 5 to 5.0.4, please be aware that the -center option may be wrong: http://redmine.gromacs.org/issues/1698 (g_density is also wrong for NPT simulations in previous versions, but for other reasons) This is in addition to the

Re: [gmx-users] Steered MD simulation of drug molecules across the plasma membrane in gromacs 5.0.4

:54 AM, Christopher Neale wrote: Dear Mahender: It's a real pity that the pull_geometry = position has been removed. So now it's impossible to do umbrella sampling of a solute across a lipid bilayer properly? Anyway, I see a note about this removal here ( http://redmine.gromacs.org/issues

Re: [gmx-users] Steered MD simulation of drug molecules across the plasma membrane in gromacs 5.0.4

Dear Mahender: It's a real pity that the pull_geometry = position has been removed. So now it's impossible to do umbrella sampling of a solute across a lipid bilayer properly? Anyway, I see a note about this removal here ( http://redmine.gromacs.org/issues/1346 ), though no reason is given.

Re: [gmx-users] umbrella sampling and PMF calculation by using pull-geometry=direction in gromacs 5.0.4

Better yet, repeat something that is already out there in the literature. PMFs for water, lipids, and some amino acid side chains across the bilayer have been tested extensively. Chris. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se

Re: [gmx-users] umbrella sampling and PMF calculation by using pull-geometry=direction in gromacs 5.0.4

...@gromacs.org. -- Message: 3 Date: Sun, 3 May 2015 12:25:01 + From: Christopher Neale chris.ne...@alum.utoronto.ca To: gmx-us...@gromacs.org gmx-us...@gromacs.org Subject: Re: [gmx-users] umbrella sampling and PMF calculation by using pull-geometry

Re: [gmx-users] Steered MD simulation of drug molecules across the plasma membrane in gromacs 5.0.4

on the setting which I have mentioned above and their correctness. (there may be chances that I may have understood the parameters wrongly), and from this simulation I want to do the umbrella sampling for free energy calculation. with regards Mahender Singh Hi Christopher Neale and Justin I

[gmx-users] Gas phase simulation

) if not then why not (i.e., adjust the parameters). Chris. From: gozde ergin gozdeeer...@gmail.com Sent: 05 May 2015 07:16 To: Christopher Neale Subject: Fwd: About 2011 paper -- Forwarded message -- From: gozde ergin gozdeeer...@gmail.commailto:gozdeeer

Re: [gmx-users] umbrella sampling and PMF calculation by using pull-geometry=direction in gromacs 5.0.4

Take a look at profiles in the literature for arginine across a bilayer. It has a maximum at the center. Probably true for any molecule with a large charge/molecular weight ratio. For more help you'd likely have to reveal your system and provide an image of the PMF. However, there is no reason

Re: [gmx-users] Gas phase simulation

to organic layer which prevent this gas phase molecule to be absorbed by bulk phase. However I can not capture this maxima on free energy if I do not restraint my organic molecules. Here you can find my density profile for water and organic layer. ​ On Tue, May 5, 2015 at 2:32 PM, Christopher Neale

Re: [gmx-users] Gas phase simulation

and organic phase. I also put their snapshots from VMD. There are two more figures to check the statistics which are bsProfs and bsResult. There is also histogram image. On Tue, May 5, 2015 at 5:40 PM, Christopher Neale chris.ne...@alum.utoronto.ca wrote: post the images elsewhere and the post

Re: [gmx-users] gromacs-5.0.4 installation problem

Gromacs only notified you about turning off the GPU code, that was not an error. The error was the AVX vs. SSE4.1 problem. Not sure why you are getting that since I thought cmake would get these things straight. Chris. From:

Re: [gmx-users] Gas phase simulation

at 2:34 PM, Christopher Neale chris.ne...@alum.utoronto.ca wrote: Why do images 4 and 5 show a length of 20 nm but your PMF and histograms only go 5 nm? Based on Figs 4 and 5, 5 nm is insufficient to go from bulk water through the organic solvent to vacuum. Also, what are your groups

Re: [gmx-users] Subject: Re: how to avoid multiple 'aprun' on batch job script?

If your sysadmin has a hard rule against multiple aprun instances then that is something that we obviously can't fix ;) However, I will note that (with mpirun) on some clusters multiple sequential instances will work and on other clusters it simply does not. The issue on some of these clusters

Re: [gmx-users] umbrella sampling and PMF calculation by using pull-geometry=direction in gromacs 5.0.4

I see your confusion now. The PMF is actually defined as dG(x) + C, where C is some unknown constant. Therefore, in the left figure, you have dG_a(x) + C_a and on the right you have dG_b(x) + C_b, so if the profiles have the same shape then the PMFs can be identical if C_a is different from

[gmx-users] mdp options for charmm27 force field in gromacs version 4.6.7

Dear Users: I would like to use the charmm27 force field in gromacs version 4.6.7 and I would like to know if it is possible to get the proper treatment of vdw interactions. Information for gromacs 5 is here: http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM However,

Re: [gmx-users] mdp options for charmm27 force field in gromacs version 4.6.7

Lemkul jalem...@vt.edu Sent: 18 May 2015 20:29 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] mdp options for charmm27 force field in gromacs version 4.6.7 On 5/18/15 2:21 PM, Christopher Neale wrote: Dear Users: I would like to use the charmm27 force field in gromacs version 4.6.7 and I

Re: [gmx-users] (no subject)

Dear Bahare: this is not necessarily a problem. If what you are saying is that in two separate runs of the same system from the same coordinates you got different trajectories then this is expected under most conditions: http://www.gromacs.org/Documentation/Terminology/Reproducibility

Re: [gmx-users] angle distribution between a vector and Z axis

You can get the coordinates of all P and N atoms with g_traj and then write an awk script to process the output (determine the angles and make the histogram). But if g_angle in gromacs 5 can do it, then why not just use that? Many analysis programs will take a .gro file for the -s option, and

Re: [gmx-users] calculating free energy

How about temperature replica exchange with de novo folding, then convert the probabilities of the folded and unfolded states into a free energy difference? You'll obviously need to be really careful about cutting off a sufficient amount of initial simulation time as equilibration, but you

Re: [gmx-users] crashed runs

Dear Bahare: what data does not match what other thing? What type of crash did you encounter? What version of gromacs? etc... Please provide as much detail as you can. As your question stands, we could as easily answer the question how deep is water? Chris.

Re: [gmx-users] make_ndx question

what about editconf -f orig.pdb -o new.gro followed by figuring out the new residue numbers and running make_ndx on new.gro ? I don't think you'll need the -resnr 1 editconf flag, but if you run into other problems then you might try that. Chris.

Re: [gmx-users] PBC issue

If you just want to make a new, larger water box, try editconf to make the box larger and then genbox to add water. Any help beyond than that requires us to guess at at least four questions: What is an unloading simulation How did you pull a protein What exactly do you mean by both ends of the

[gmx-users] Why is there a difference between an angle of 0 or 180 deg. for a type 9 proper dihedral with multiplicity of 2?

Dear Gromacs users: I have been working on creating a topology for an exotic molecule. It contains aromatic rings and my parameters always seemed to allow the rings to buckle and become non-planer, much like a glucose ring would (though a little less extensively). However, I have managed to

Re: [gmx-users] Why is there a difference between an angle of 0 or 180 deg. for a type 9 proper dihedral with multiplicity of 2?

Verified same behaviour in gromacs 4.6.7 and 5.0.5 for the Phe-Phe system. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Christopher Neale chris.ne...@alum.utoronto.ca Sent: 05 July

Re: [gmx-users] Why is there a difference between an angle of 0 or 180 deg. for a type 9 proper dihedral with multiplicity of 2?

on behalf of Justin Lemkul jalem...@vt.edu Sent: 04 July 2015 09:41 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Why is there a difference between an angle of 0 or 180 deg. for a type 9 proper dihedral with multiplicity of 2? On 7/4/15 3:32 AM, Christopher Neale wrote: Dear Gromacs users: I

Re: [gmx-users] Why is there a difference between an angle of 0 or 180 deg. for a type 9 proper dihedral with multiplicity of 2?

with multiplicity of 2? On 7/5/15 12:56 AM, Christopher Neale wrote: Dear Justin: Thank you for your help. I am glad to see that I was not way out to lunch in my interpretation of multiplicity and proper dihedral angles. First, the out-of-plane motions are not minor. Even just in EM

Re: [gmx-users] Why is there a difference between an angle of 0 or 180 deg. for a type 9 proper dihedral with multiplicity of 2?

with multiplicity of 2? On 7/5/15 9:10 AM, Christopher Neale wrote: Dear Justin: here is a topology followed by initial coordinates (in which the rings of both Phe are planar, straight out of molefacture/pdb2gmx). Run this in EM or MD and the SC ring of Phe #1 will distort. However, replace 0

[gmx-users] Trojan version of putty software

Not gromacs specific, but I thought it was worth posting here. Basically, if you use putty, check the about button and make sure that you don't see the text unidentified build. http://blogs.cisco.com/security/trojanized-putty-software -- Gromacs Users mailing list * Please search the archive

[gmx-users] links errors at 700 or 800 K

Dear Users: I have a system with an 8-mer peptide in a box of water. After a 2-ns npt equilibration, I run 100 ns of nvt at various temperatures (300-800 K) in preparation for a REMD simulation. I am using velocity langevin for temperature control. Everything is fine for =600 K. Above that,

Re: [gmx-users] pdb2gmx: can we use a file to specify the protonation instead of using -inter?

Dear Cheng: You can define protonation states like this: echo 0 1 2 | pdb2gmx -ff amber99sb-ildn -water tip3p -his That will give you, in order for three HIS residues: 0. H on ND1 only (HID) 1. H on NE2 only (HIE) 2. H on ND1 and NE2 (HIP) You can also use -inter, but you'll need to do a

[gmx-users] build nuance in gmx5 (avoiding file INSTALL cannot find gmx)

Dear Users: This is just a note about compiling gromacs 5 so that the solution can be found by others if they need it. I used to compile gromacs like this: download and unpack tarball cd gromacs-5.0.5 mkdir source mv * source mkdir exec cd exec ** run my build script from here, using

Re: [gmx-users] build nuance in gmx5 (avoiding file INSTALL cannot find gmx)

suggest: http://www.gromacs.org/Documentation/Installation_Instructions_5.0#quick-and-dirty-installation -- Szilárd On Thu, May 21, 2015 at 5:11 PM, Christopher Neale chris.ne...@alum.utoronto.ca wrote: Dear Users: This is just a note about compiling gromacs 5 so that the solution can be found

Re: [gmx-users] Segmentation fault (core dumped) version 4.6.*

Dear Carlos: Are you using a .top file from gromacs 5 with your gromacs 4 runs? If so, try regenerating your topology (and .itp files) using gromacs 4 (with GMXLIB set correctly). Not sure if that would even cause a problem, but it seems like it probably would and is the only thing that comes

Re: [gmx-users] PMF using umbrella sampling and Gromacs 5.0 (Eudes Fileti)

/ -- Message: 4 Date: Wed, 22 Jul 2015 14:56:50 + From: Christopher Neale chris.ne...@alum.utoronto.ca To: gmx-us...@gromacs.org gmx-us...@gromacs.org Subject: Re: [gmx-users] PMF using umbrella sampling and Gromacs 5.0 Message-ID

Re: [gmx-users] PMF using umbrella sampling and Gromacs 5.0

Dear Eudes: There are two issues: The first issue is the fact that you've got a sampling problem near the bilayer center. The second issue is the periodic bumps that you see in your PMFs. I'll take the second part first. The source of the periodic bumps in PMFs from umbrella sampling is, to

[gmx-users] REMD and distance restraints problem in gmx 4.6.7

Dear Users: I have a system with many distance restraints, designed to maintain helical character, e.g.: [ distance_restraints ] 90 33 1 1 2 2.745541e-01 3.122595e-01 999 1.0 97 57 1 2 2 2.876300e-01 2.892921e-01 999 1.0 114 73 1 3 2 2.704403e-01 2.929642e-01 999 1.0 ... Distance restraints are

Re: [gmx-users] REMD and distance restraints problem in gmx 4.6.7

raham <mark.j.abra...@gmail.com> Sent: 18 September 2015 04:11 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] REMD and distance restraints problem in gmx 4.6.7 Hi, On Fri, Sep 18, 2015 at 6:27 AM Christopher Neale < chris.ne...@alum.utoronto.ca> wrote: > Dear Users: > >

Re: [gmx-users] problem about distance restraint in REMD simulation

This is essentially what I have done and it worked fine for me. In fact, not being as clever as Mark I simply commented out that entire if/gmx_fatal block of code and use this modified code only in cases where I an not concerned about other side-effects. It is stable for >500 ns/replica.

Re: [gmx-users] Decreased Area Per Lipid for Lipid Bilayer obtained from CHARMM-GUI

In future posts, it is best to copy and paste your .mdp file because we can not all get attachments from the list. Regarding your results, it is my understanding that the CHARMM-GUI has parameters for, and can build, many lipids systems whose parameters have not been completely validated by

Re: [gmx-users] water density

I am fairly confused about what you want to obtain and what you have done, but is it possible that you simply have not turned on pressure coupling? General procedure even if you eventually want to do constant volume simulation is to do some equilibration with constant pressure to get densities

Re: [gmx-users] Lipid parameterization

You might see if CHARMM_GUI has parameters for it. This is not to say that they will be amazing parameters, as I have not looked into their approach to generate parameters and it may well be rational cut and paste, but they do have parameters for loads of lipids. If they don't have parameters,

Re: [gmx-users] Decreased Area/Lipid of Lipid Bilayer from CHARMM-GUI

ithm = LINCS continuation = yes ; nstcomm = 100 comm_mode = linear comm_grps = MEMB SOL_ION ; refcoord_scaling = com Thanks, Nidhin Thomas University of Houston > Message: 4 > Date: Mon, 13 Jun 2016 17:51:43 + > From: Christopher Neale <chris.ne...@alum.utoronto.ca> &

Re: [gmx-users] Lipid parameterization

om: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin Lemkul <jalem...@vt.edu> Sent: 14 June 2016 14:35:26 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Lipid parameterization On 6/14/16 2:04 PM, Christopher Neal

Re: [gmx-users] PMF steadily increasing

(1) Are the protein and peptide really never interacting at d=7 nm? I presume you've got a peptide that would be maybe 5 nm long when fully extended, and your dG minimum is at 1.5 nm, so giving half the peptide length that would imply possible contact at 4 nm, so I expect 7 nm is sufficient,

Re: [gmx-users] Analyse REMD

Dear Ouyang: There is a script in the gromacs package (at least up to 5.1.2) called demux.pl . You can use it to get more human friendly information out of your REMD runs ( see http://www.gromacs.org/Documentation/How-tos/REMD for some very sparse info on demux.pl ). Basically you feed it the

Re: [gmx-users] compile 2016-beta2 failed

cicc is a cuda compiler (i.e., nvcc) From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Albert Sent: 17 June 2016 14:55:02 To: gmx-us...@gromacs.org Subject: Re:

Re: [gmx-users] PMF steadily increasing

gt; 2016-06-15 19:01 GMT+02:00 Christopher Neale <chris.ne...@alum.utoronto.ca > >: > >> (1) Are the protein and peptide really never interacting at d=7 nm? I >> presume you've got a peptide that would be maybe 5 nm long when fully >> extended, and your dG minimum is at 1.5 nm, so

Re: [gmx-users] Basic Understanding about Gromacs C library

Writing your own analysis tool in template.c might not be the best solution either. You have to worry about things like pbc breaking and you in many cases need to write routines that already exist elsewhere. I suggest looking into standalone analysis kits such as http://loos.sourceforge.net/ or

[gmx-users] where are the release notes for versions 5.1.1 and 5.1.2?

Dear Users: I find release notes for gromacs 5.1 here: http://manual.gromacs.org/documentation/5.1/ReleaseNotes/index.html . The text on that site ( "These release notes document the functionality changes that have taken place in GROMACS since version 5.0." ) is kind of vague and I am not

Re: [gmx-users] where are the release notes for versions 5.1.1 and 5.1.2?

rsions 5.1.1 and 5.1.2? Hi, See http://manual.gromacs.org/documentation/. Mark On Wed, Mar 30, 2016 at 7:42 PM Christopher Neale < chris.ne...@alum.utoronto.ca> wrote: > Dear Users: > > I find release notes for gromacs 5.1 here: > http://manual.gromacs.org/documentati

Re: [gmx-users] *.pdb file for the Tip4p/ice model

Need it for what? To solvate a solute with genbox or for some other sytem setup needs? Common protocol would be to simply use tip4p.gro and then to equilibrate it with the new tip4p/ice parameters. tip4p.gro is in share/gromacs/top/ Chris. From:

[gmx-users] desired usage of verlet-buffer-tolerance with charmm ff?

Dear users: Charmm mdp options are listed here: http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM with the following values: constraints = h-bonds cutoff-scheme = Verlet vdwtype = cutoff vdw-modifier = force-switch rlist = 1.2 rvdw = 1.2 rvdw-switch = 1.0 coulombtype = PME

Re: [gmx-users] wanted to fix cpn in lipid layer MD, -position/distance restrains

This is not enough detail for us to know what the problem is. Did you set things up correctly so that posre_cpn.itp is actually used? You can check by gmx energy and see if you have restraint energies there. To use these restraints your .top file needs to #include "posre_cpn.itp" , which you

Re: [gmx-users] desired usage of verlet-buffer-tolerance with charmm ff?

sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Szilárd Páll <pall.szil...@gmail.com> Sent: 08 April 2016 06:42 To: Discussion list for GROMACS users Subject: Re: [gmx-users] desired usage of verlet-buffer-tolerance with charmm ff? On Thu, Apr 7, 2016 at 9:55

[gmx-users] correction to a typo in the electric conversion factor in one place in the manual

Dear Mark: The value of f listed under eq. 4.11 is wrong in the gmx 5.1.2 manual. The correct value is reported on the bottom of page 7 at the start of section 2.2 on "MD Units". I verified this using the values in src/gromac/math/units.h. -- Gromacs Users mailing list * Please search the

Re: [gmx-users] Looking for the source of the H-REMD slowdown when decoupling a lot of atoms

systems to create the alchemical intermediates. Changing the way the code is structured would again require some significant changes and time. On Thu, Mar 31, 2016 at 10:49 AM, Christopher Neale <chris.ne...@alum.utoronto.ca> wrote: > Dear Szilárd, Mark, and Michael: > > Thank you for you

Re: [gmx-users] a question related to minim.mdp

It depends on what you want to do. If you simply want to minimize the system so that the dynamics will be stable in MD, then I have never needed more than 500 steps of minimization (though in some cases I find it necessary to use flexible waters and solutes via the mdp options define=-DFLEXIBLE

Re: [gmx-users] Looking for the source of the H-REMD slowdown when decoupling a lot of atoms

. > > > > I don't see a particularly viable way around this for now. The only > > thing I can think of splitting the neighborlists into two force calls, > > and scaling the forces and energies coming out of those. That would > > be a huge pain. > > > > O

Re: [gmx-users] Suggestion to update online .mdp options for pull code

Mark Abraham <mark.j.abra...@gmail.com> Sent: 31 March 2016 14:37 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Suggestion to update online .mdp options for pull code Hi, On Thu, 31 Mar 2016 19:23 Christopher Neale <chris.ne...@alum.utoronto.ca> wrote: > Dear develope

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