Re: [gmx-users] ramachandran plot
Hi Tsjerk,
I was wondering how did you get the input.dat file? did you got it from
grace/xmgrace? I was able to save the plot in .ps or .png format file.
However whenever I tried to run kde2d.r I was getting an error:
Please see below:
./kde2d.r ramachandran.png ramachandran-2.png
./kde2d.r: line 11: syntax error near unexpected token `('
./kde2d.r: line 11: `args - commandArgs()'
what could be wrong?
best regards
Urszula
Hi Urszula,
Save the following as kde2d.r and make it executable. Then you can run
./kde2d.r rama.dat rama.png
Cheers,
Tsjerk
kde2d.r
#!/usr/bin/env Rscript
# Script for drawing 2D combined linear/circular KDE plots.
#
# (c)2014 Tsjerk A. Wassenaar
# Friedrich-Alexander University of Erlangen-Nuremberg
args - commandArgs()
args - args[-(1:match(--args, args))]
# MASS library is needed for bandwidths
require(MASS)
# This 2D circular KDE function was developed for correct handling
# of bivariate angular data as part of the orientational analysis
# used with DAFT (Manuscript submitted).
kde2d - function (x, y, h, n = 25, xlim, ylim, circular=TRUE, phase=0)
{
if (length(y) != length(x))
stop(data vectors must be the same length)
n- rep(n, length.out = 2L)
phase- rep(phase, length.out = 2L)
circular - rep(circular, length.out = 2L)
s - which(!is.na(x) | !is.na(y))
x - x[s]
y - y[s]
nx - length(x)
if (any(!is.finite(x)) || any(!is.finite(y)))
stop(missing or infinite values in the data are not allowed)
if (circular[1])
x - (x+180)%%360-180
if (circular[2])
y - (y+180)%%360-180
if (missing(xlim))
xlim - if (circular[1]) c(-180,180) else range(x)
if (missing(ylim))
ylim - if (circular[2]) c(-180,180) else range(y)
if (any(!is.finite(c(xlim,ylim
stop(only finite values are allowed in 'xlim' and 'ylim')
h - if (missing(h))
c(bandwidth.nrd(x), bandwidth.nrd(y))
else rep(h, length.out = 2L)
if (any(h = 0))
stop(bandwidths must be strictly positive)
h - h/4
if (circular[1])
{
gx - seq.int(-180, 180, length.out = n[1L])
ax - ((outer(gx, x-phase[1], -)+180)%%360-180)/h[1L]
gx - gx + phase[1]
}
else
{
gx - seq.int(xlim[1], xlim[2], length.out = n[1L])
ax - outer(gx, x, -)/h[1L]
}
if (circular[2])
{
gy - seq.int(-180, 180, length.out = n[2L])
ay - ((outer(gy, y-phase[2], -)+180)%%360-180)/h[2L]
gy - gy + phase[2]
}
else
{
gy - seq.int(ylim[1], ylim[2], length.out = n[2L])
ay - outer(gy, y, -)/h[2L]
}
z - tcrossprod(matrix(dnorm(ax), , nx), matrix(dnorm(ay), , nx))/(nx
*
h[1L] * h[2L])
list(x = gx, y = gy, z = z)
}
# Color gradients for coloring density plots
rng - seq(0,1,length.out=100)
white2red - rgb(1,rev(rng),rev(rng))
blue2white- rgb(rng,rng,1)
# Rainbow
magenta2red - rgb(1,0,rev(rng))
red2yellow- rgb(1,rng,0)
yellow2green - rgb(rev(rng),1,0)
green2cyan- rgb(0,1,rng)
cyan2blue - rgb(0,rev(rng),1)
red2orange- rgb(1,0.5*rng,0)
orange2yellow - rgb(1,0.5+0.5*rng,0)
data - read.table(args[1])
d- kde2d(data[,1],data[,2])
## Plotting density images
# Here the density images are prepared and written to file. The first one
(WT) is explained in detail:
#---Start of image---
# Wildtype
# Start a 1200x1200 png file, with a font size (for labels) of 40 points
# Changing the resolution requires changing the font size to keep the
relative size.
png(
args[2],
width=1200,
height=1200,
pointsize=40
)
# Write an image of the density for WT
image(
d$x, d$y, d$z, # Image data X/Y and intensity (Z)
zlim=c(0,max(d$z)),# Limits for coloring
xlab=expression(phi), # X-label text. expression(beta) gives the
greek
character
ylab=expression(psi), # Y-label text.
main=, # Main title. Can be set to to suppress
title.
bty=n, # Surrounding box type. To draw a thicker box,
the box is here suppressed, using n for None.
col=c(white2red,red2orange,orange2yellow)
)
box(lwd=3) # Add a box with a thicker line. Change this to
match the resolution of the imge.
# Add points
points(data[,1], data[,2], pch=., cex=1)
# Add contour lines
contour(
d$x, d$y, d$z,
zlim=c(0,max(d$z)),
add=TRUE, # If add=FALSE (default), then 'contour' starts
a new plot.
labels=, # Suppress labels on contour lines
labcex=0.001, # To avoid gaps in the controu lines (because
of
the empty label), set the label size very small
nlevels=20,# Number of lines to draw, between range of
'zlim'
lwd=3 # Width of contour lines. Set to 3 to match png
[gmx-users] Residue Selection
Hi, I have made and I have then clustered my results based upon this selection of residues. This was performed like this: g_cluster -f protein_nojump_rt.xtc -s protein.tpr -n index.ndx -o rmsd-clust.xpm -g cluster.log -dist rmsd-dist.xvg -ev rmsd-eig.xvg -sz clust-size.xvg -tr clust-trans.xpm -ntr clust-trans.xvg -clid clust-id.xvg -cl clusters.pdb -method gromos -cutoff 0.1 Is there a way to do this but also print out the remaining protein to the resultant clusters.pdb? As currently this file includes only the binding site residues in index.ndx. Thanks Michael Carter The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Residue Selection
Hi, Not to worry. I have create the rmsd matrix using g_rms and this allows you to then write the entire protein to the clusters.pdb with the RMSD of the binding site residues being used. Mike On 18/11/2014 09:15, Michael Carter michael.car...@icr.ac.uk wrote: Hi, I have made and I have then clustered my results based upon this selection of residues. This was performed like this: g_cluster -f protein_nojump_rt.xtc -s protein.tpr -n index.ndx -o rmsd-clust.xpm -g cluster.log -dist rmsd-dist.xvg -ev rmsd-eig.xvg -sz clust-size.xvg -tr clust-trans.xpm -ntr clust-trans.xvg -clid clust-id.xvg -cl clusters.pdb -method gromos -cutoff 0.1 Is there a way to do this but also print out the remaining protein to the resultant clusters.pdb? As currently this file includes only the binding site residues in index.ndx. Thanks Michael Carter The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Umbrella Sampling gromacs 5.0 error
On 11/17/14 11:02 PM, Alexander Law wrote: Dear vmx-users I am running through Dr Lemkul's umbrella sampling tutorial and applying this to my own structure. I have problem with the pull simulation command: grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt -o pull.tpr I receive this error message back: Ignoring obsolete mdp entry 'title' Ignoring obsolete mdp entry 'optimize_fft' Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed' ERROR: pull-coord1-groups should have 2 components WARNING 1 [file md_pull.mdp, line 62]: Unknown left-hand 'pull-group0' in parameter file WARNING 2 [file md_pull.mdp, line 62]: Unknown left-hand 'pull-group1' in parameter file WARNING 3 [file md_pull.mdp, line 62]: Unknown left-hand 'pull_rate1' in parameter file WARNING 4 [file md_pull.mdp, line 62]: Unknown left-hand 'pull_k1' in parameter file NOTE 2 [file md_pull.mdp]: With Verlet lists the optimal nstlist is = 10, with GPUs = 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. NOTE 3 [file md_pull.mdp]: nstcomm nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy NOTE 4 [file md_pull.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 -- Fatal error: Group Protein referenced in the .mdp file was not found in the index file. Group names must match either [moleculetype] names or custom index group names, in which case you must supply an index file to the '-n' option of grompp. My Index file is set up properly, with force being applied to Chain_A, and Chain_B is my static reference: 0 Chain_B : 1290 atoms 1 Chain_A : 110 atoms The fatal error is due to the fact that you've deleted the other necessary groups. You should add Chain_A and Chain_B to an index file, but not delete the other groups. The md_pull.mdp remains the same: ; Pull code pull= umbrella pull_geometry = distance ; simple distance increase pull_dim= N N Y pull_start = yes ; define initial COM distance 0 pull_ngroups= 1 pull_group0 = Chain_B pull_group1 = Chain_A pull_rate1 = 0.01 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 1000 ; kJ mol^-1 nm^-2 Any advice on how to treat this problem is appreciated. Regarding the .mdp keywords, note from the first page of the tutorial: PLEASE NOTE: This tutorial has NOT been updated to reflect the new selection syntax and .mdp options introduced in GROMACS 5.0. Use an older version (4.6.x) or check the manual for the new syntax; it doesn't differ much. I just haven't had the chance to make the changes and verify that things still work as expected. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] adding ions in Gromacs 4.6.5
On 11/18/14 1:47 AM, soumadwip ghosh wrote: Dear Justin, thanks for your reply. I really dont know how to create the .itp file from the .pdb file of the TMA cation. Do I need a topology builder? After making the .itp file, how should I proceed? If I have to add it by genion, then I guess the tma.itp must be a part of the ions.itp file of the forcefield directory, right? You can't add polyatomic ions via genion. They have to be inserted with genbox -ci -nmol (gmx insert-molecules in 5.0). You need to build the topology somehow; for CHARMM I suggest ParamChem. Amines are well covered in CGenFF and CHARMM. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Dihedral restraints
Dear gromacs users, I am working in a system composed by a protein in a solvated box. It is a coarse-grained model (Martini ff). The protein has an amyloid part (strand-loop-strand), at first I tried to simulated this without restraints but the structure collapsed, then I used position restraints as a result it kept the structure but due to the type of restraint I applied it is fix in the box without possibility of motion (translate, rotate). I was reading and maybe using dihedral restraints I can solve this problem. Someone knows if it is possible? In summary, what I want is keep the amyloid part in its correct structure but allow its movement within the box. Thanks in advance! Adriana -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Tricky implementation of REST in GROMACS 4.6.5
I'm trying to run a hamiltonian REMD simulation at constant temperature, but i have problems installing plumed with hrex as suggested by Bussi ( https://groups.google.com/forum/#!msg/plumed-users/ROngJ1UyfHI/-nlna83yTy0J ). The thing that i was thinking so is to prepare one topology for every replica with pertrurbed values of bonds, lenght, dihedral, charges etc, then make individual tpr files and then run the simulation with multidir and replex. The problem is that if i keep the temperature 300K for every replica, gromacs tells me that there is nothing to exchange and the simulation dies. So i was wondering, as gromacs needs different temperatures for starting the simulations, is it acceptable to trick him introducing for every replica a slightly different temperature (i have to run 32 replicas, i was thinking to run the first replica with unperturbed hamiltonian at 300K and then increment by 0.1 K every replica) ? Would this perturbation affect the exchange probability of 2 replicas significantly? Thank you in advance for your time! -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Changing constraints algorithm.
Dear all, A question arises to me when thinking about the more robustness of LINCS with respect to SHAKE: is it well known that LINCS preserves the symplecticness of the Verlet integrators? Thank you very much. Best regards, Mario 2014-10-08 22:31 GMT+02:00 Mark Abraham mark.j.abra...@gmail.com: You should start by following all the advice here http://www.gromacs.org/Documentation/Terminology/Blowing_Up Mark On Wed, Oct 8, 2014 at 9:50 PM, Dawid das add...@googlemail.com wrote: Well, what happens in my system is that water molecule which is actually near the edge of solvation box cannot bo settled after ca. 50 ns of simulation. Obviously I use periodic boundary conditions. Could you give me any tip about what is wrong if I provide you with files you need? If so, what files would you need? Best wishes, Dawid Grabarek PS I read samowhere, that it may be due to fact that this water molecule is hit by something and this water did not expect it. But I tried to use brutal force approach and to restart the calculations couple of times but each time I run into the same error, although for different molecule. 2014-10-08 13:33 GMT+02:00 Justin Lemkul jalem...@vt.edu: On 10/8/14 7:24 AM, Dawid das wrote: Dear gromacs experts, Is it allowed to change constraints algorithm (e.g. from LINCS to SHAKE) during MD simulation? Let's say that simulation crashes because LINCS constraints are not satisfied. Can I go from LINCS to shake in the middle of simulation and restart calculations from the previous point? If LINCS is failing, it's not because you need a different constraint algorithm; it's because something physically unrealistic is happening, and the constraints are the first thing to fail. LINCS is more robust than SHAKE, so if you're trying to circumvent this problem by moving to SHAKE, I'd say it's likely futile. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Tricky implementation of REST in GROMACS 4.6.5
On 11/18/14 10:44 AM, Carlo Martinotti wrote: I'm trying to run a hamiltonian REMD simulation at constant temperature, but i have problems installing plumed with hrex as suggested by Bussi ( https://groups.google.com/forum/#!msg/plumed-users/ROngJ1UyfHI/-nlna83yTy0J ). The thing that i was thinking so is to prepare one topology for every replica with pertrurbed values of bonds, lenght, dihedral, charges etc, then make individual tpr files and then run the simulation with multidir and replex. The problem is that if i keep the temperature 300K for every replica, gromacs tells me that there is nothing to exchange and the simulation dies. So i was wondering, as gromacs needs different temperatures for starting the simulations, is it acceptable to trick him introducing for every replica a slightly different temperature (i have to run 32 replicas, i was thinking to run the first replica with unperturbed hamiltonian at 300K and then increment by 0.1 K every replica) ? Would this perturbation affect the exchange probability of 2 replicas significantly? Thank you in advance for your time! I think it makes more sense to simply make use of the free energy code in this case to do the HREX. You can define any number of lambda states for scaling of LJ, Coulombic, bonded, etc. interactions and simply define each replica to be one of those lambda states. The replica exchange code works fine when you define different lambda states, even at the same temperature. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Wrong profile obtained in umbrella sampling tutorial
On 11/18/14 10:58 AM, Victor Rosas Garcia wrote: Hello everybody, I have followed Justin Lemkul's tutorial on umbrella sampling, but when I do the data analysis, my energy profile looks wrong. Please see the profile: https://uanledu-my.sharepoint.com/personal/victor_rosasgr_uanl_edu_mx/Documents/Shared%20with%20Everyone/profile.png and the histogram: https://uanledu-my.sharepoint.com/personal/victor_rosasgr_uanl_edu_mx/Documents/Shared%20with%20Everyone/histo.png I would be grateful on any pointers about how to start diagnosing what is wrong. I am using Gromacs 4.5.4 under linux. Please post your images somewhere public that does not require Office365 credentials. Note that the tutorial will not *exactly* reproduce the PMF profile, since I used a slightly different window setup to produce it (described in the paper referenced in the tutorial). -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Dihedral restraints
On 11/18/14 10:38 AM, Adriana Garro wrote: Dear gromacs users, I am working in a system composed by a protein in a solvated box. It is a coarse-grained model (Martini ff). The protein has an amyloid part (strand-loop-strand), at first I tried to simulated this without restraints but the structure collapsed, then I used position restraints as a result it kept the structure but due to the type of restraint I applied it is fix in the box without possibility of motion (translate, rotate). I was reading and maybe using dihedral restraints I can solve this problem. Someone knows if it is possible? Sure it is. See manual section 4.3.4 and Table 5.5. There's an online how-to at http://www.gromacs.org/Documentation/How-tos/Dihedral_Restraints but it may be outdated. See if it works (the manual seems to indicate that it is easier than what is stated there) and please suggest changes if it doesn't! -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Wrong profile obtained in umbrella sampling tutorial
Sorry about that Office messup. These are the new links: histogram https://drive.google.com/file/d/0B2K7fedV_ZFzaFlOMWh1QXFTa2s/view?usp=sharing profile https://drive.google.com/file/d/0B2K7fedV_ZFzSm16bnlJSUFGVms/view?usp=sharing I understand that the profile may not look exactly the same between different runs, but I do think the difference is large enough to think something is amiss. Regards Victor 2014-11-18 13:14 GMT-06:00 Justin Lemkul jalem...@vt.edu: On 11/18/14 10:58 AM, Victor Rosas Garcia wrote: Hello everybody, I have followed Justin Lemkul's tutorial on umbrella sampling, but when I do the data analysis, my energy profile looks wrong. Please see the profile: https://uanledu-my.sharepoint.com/personal/victor_rosasgr_uanl_edu_mx/Documents/Shared%20with%20Everyone/profile.png and the histogram: https://uanledu-my.sharepoint.com/personal/victor_rosasgr_uanl_edu_mx/Documents/Shared%20with%20Everyone/histo.png I would be grateful on any pointers about how to start diagnosing what is wrong. I am using Gromacs 4.5.4 under linux. Please post your images somewhere public that does not require Office365 credentials. Note that the tutorial will not *exactly* reproduce the PMF profile, since I used a slightly different window setup to produce it (described in the paper referenced in the tutorial). -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Wrong profile obtained in umbrella sampling tutorial
On 11/18/14 3:23 PM, Victor Rosas Garcia wrote: Sorry about that Office messup. These are the new links: histogram https://drive.google.com/file/d/0B2K7fedV_ZFzaFlOMWh1QXFTa2s/view?usp=sharing profile https://drive.google.com/file/d/0B2K7fedV_ZFzSm16bnlJSUFGVms/view?usp=sharing I understand that the profile may not look exactly the same between different runs, but I do think the difference is large enough to think something is amiss. Sampling in window 1 is a little odd - the distribution is incredibly narrow, if you can even call it a distribution at all. Make sure everything is OK in that window. In the absence of a well-defined minimum, you're not going to get a sensible profile. People's mileage varies as far as recapitulating that PMF curve, but I have received confirmation from at least two other people that the PMF can be reproduced following the method in the paper. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] help to solve this problem
Dear gromacs users: I'm trying to run a MD simulation using gromacs 4.6.5 in a cluster but when I submit my job using the following script: /bin/bash #Name of your job #PBS -N PlmII+Inhibitor_free #number of nodes you are using #PBS -l nodes=8 #time #PBS -l walltime=48:00:00 #which queue you are submitting to #PBS -q qwork@mp2 # go to our working directory cd $PBS_O_WORKDIR # add module module rm mvapich2_intel64/1.6_ofed module add openmpi_intel64/1.4.3_ofed module rm gromacs64/4.5.4_ompi module add gromacs64/4.6.5_ompi # choose mpi-tasks per node *** there are 24 cores/node export ppn=24 # set your executable file myExe=`which mdrun_mpi` # start the application export RUN_NAME=PlmII+Inhibitor_free export P4_GLOBMEMSIZE=2 #export OPTIONS= -cpi PlmII+Inhibitor_free.cpt -dlb yes #export OPTIONS= -cpi prot_md.cpt -dlb yes #actual command line mpiexec -n $[PBS_NUM_NODES*ppn] -npernode $ppn $myExe -deffnm $RUN_NAME $OPTIONS echo Job finished at: `date` # I have the following error: cp2456:22501] *** Process received signal *** [cp2456:22501] Signal: Segmentation fault (11) [cp2456:22501] Signal code: (128) [cp2456:22501] Failing at address: (nil) [cp2456:22501] [ 0] /lib64/libpthread.so.0() [0x3638c0f710] [cp2456:22501] [ 1] /opt/gromacs64/4.6.5/bin/../lib/libmd_mpi.so.8(nbnxn_kernel_simd_4xn_tab_comb_lb_energrp+0x4183) [0x2b88117267c3] [cp2456:22501] [ 2] /opt/gromacs64/4.6.5/bin/../lib/libmd_mpi.so.8(nbnxn_kernel_simd_4xn+0x4b1) [0x2b88117a4951] [cp2456:22501] [ 3] /opt/intel/composerxe-2011.5.220/compiler/lib/intel64/libiomp5.so(__kmp_invoke_microtask+0x93) [0x2b88149e6b83] [cp2456:22501] *** End of error message *** -- mpiexec noticed that process rank 0 with PID 22501 on node cp2456 exited on signal 11 (Segmentation fault). with kind regards, Pedro -- ** Dr. Pedro Alberto Valiente Flores Profesor e Investigador Auxiliar Jefe Laboratorio de Bioinformática y Dinámica Biomolecular Centro de Estudios de Proteínas Facultad de Biología Universidad de La Habana Email:valie...@fbio.uh.cu Fax:+5378321321 Tel: +5378324830 ** -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Wrong profile obtained in umbrella sampling tutorial
Thanks, I'll check it out. It may be a remnant of a previous, botched, run. 2014-11-18 15:56 GMT-06:00 Justin Lemkul jalem...@vt.edu: On 11/18/14 3:23 PM, Victor Rosas Garcia wrote: Sorry about that Office messup. These are the new links: histogram https://drive.google.com/file/d/0B2K7fedV_ZFzaFlOMWh1QXFTa2s/view?usp=sharing profile https://drive.google.com/file/d/0B2K7fedV_ZFzSm16bnlJSUFGVms/view?usp=sharing I understand that the profile may not look exactly the same between different runs, but I do think the difference is large enough to think something is amiss. Sampling in window 1 is a little odd - the distribution is incredibly narrow, if you can even call it a distribution at all. Make sure everything is OK in that window. In the absence of a well-defined minimum, you're not going to get a sensible profile. People's mileage varies as far as recapitulating that PMF curve, but I have received confirmation from at least two other people that the PMF can be reproduced following the method in the paper. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] restraint the CM of a molecules in any one of the directions.
Hi All, Is there a way to restraint the CM of a molecules in any one of the directions. I have been through the manual and the user list but could not find a solution. It seems we can implement the position restraints only on atoms but not on the CM of a molecules. I want the molecule to rotate freely, applying the atomic position restraints do the job but it prevent the rotation of the molecule. Any suggestions ? Thank you. -- Cheers !!! Sridhar Kumar Kannam :) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] changing ewald_rtol
Thank you very much for the answer. On Tue, Nov 18, 2014 at 2:03 PM, Mark Abraham mark.j.abra...@gmail.com wrote: On Tue, Nov 18, 2014 at 7:38 PM, Johnny Lu johnny.lu...@gmail.com wrote: Hi. from online manual: *ewald-rtol (1e-5)* The relative strength of the Ewald-shifted direct potential at *rcoulomb* is given by *ewald-rtol*. Decreasing this will give a more accurate direct sum, but then you need more wave vectors for the reciprocal sum. Is it ok to use ewald-rtol=1e-9 for Amber99SB-ILDN forcefield? That's not a question that has a useful single answer. 1) It wasn't parameterized with any Ewald method, so any subsquent use of that method is valid only upon empirical evidence. 2) Different observables in different systems have different dependencies on the quality of the electrostatics model, and this one parameter is only part of any story. 3) A tiny magnitude of forces at the cutoff matters little if they're being added to other forces at shorter distances - and if there's more than about 5 orders of magnitude difference, then the small ones get lost in the accumulation in floating-point representation 4) Making one part of the electrostatics approximation super accurate while ignoring the other doesn't do any good when you add them together, because the largest error dominates. 5) Some other error might be more dominant still (e.g. incomplete sampling, interior residues have the same charges as exterior residues, no polarizability) Will the sum in reciprocal space become very inaccurate? Yes, like the docs say, because ewald-rtol and rcoulomb are used to compute the Ewald splitting parameter beta, which is then used in reciprocal space also. Or this will just make the simulation run slower? By itself, it's just multiplication by a different scaling factor. Fixing the issues in reciprocal space (increasing number of grid points and/or spline interpolation order) will be expensive. Mark Thanks again. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Free Energy calculation
Thank you justin is there any tutorial like kalp in dppc which i can follow how can i calculate the diffusion coefficient of ligand(drug) thanks in advance On Fri, Nov 14, 2014 at 12:04 AM, Justin Lemkul jalem...@vt.edu wrote: On 11/13/14 4:09 AM, RINU KHATTRI wrote: hello gromacs users i am working on protein ligand complex with popc membrane i want to calculate the free energy of protein and ligand i have to follow which tutorial (methane in water) but my protein is membrane protein i am also running md simulation (70 ns) i am new in free energy calculation from where i have to start after the production md or i can start from the original pdb file The free energy of protein and ligand is a rather ill-defined quantity. Are you trying to calculate binding free energy? If so, there's a huge amount of literature on this topic. It comes down to simply doing a thermodynamic cycle of the ligand in water and in the binding site. Restraints might be needed to keep the ligand bound while being decoupled, but again there's tons of papers on this topic. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
