[gmx-users] Free energy calculations with pull code and umbrella sampling
Hi All, I have one quick questions about free energy calculations via pull code+umbrella sampling. (see below for some further information on what I am trying) First of all I think Justin is right umbrella sampling is much more straightforward. In particular in my situation where I see spontaneous binding at the site I am interested in, i.e. I already have a pathway of the ion to the binding site. So what I would do now is: Skip the pull code and just use the pathway I already have for the umbrella sampling. Again my question is: Is this sensible? Of course I have to check if the spacing of the pathway is close enough (output frequency of the xtc was 10ps) but on first sight I think it is, I could easily construct ~30 intermediates from the data I already have. If I need more intermediates my approach would be to use frames I already have and only pull between the positions of those frames instead of pulling the whole way from the binding site to the bulk. On 2/5/15 6:59 AM, Kortzak, Daniel wrote: Dear All, I want to calculate the free energy of binding of a single sodium ion to a protein. I want to do this by decoupling the ion in the binding site (with the couple-moltype approach). The work-flow I have in mind is roughly: 1. Start with ion in binding site 2. Turn on position restraints (since this only one atom I don't have to care about orientation etc.) 3. Decouple (And do the same for a ion in bulk solution in another simulation.) First of all is this sensible or are there better ways of doing this? Wouldn't just using the pull code to do umbrella sampling be a much more straightforward approach? You don't have to deal with compensating for artifacts associated with the restraint potential during decoupling and removing a charge from the system. -Justin Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- 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] g_rms with two trajectories
After some further search I found this very useful script which converts
xpm to digits. This has solved my problem.
#!/usr/bin/env python
import sys
def unquote(s):
return s[1+s.find(''):s.rfind('')]
def uncomment(s):
return s[2+s.find('/*'):s.rfind('*/')]
def col(c):
color = c.split('/*')
value = unquote(color[1])
color = unquote(color[0]).split()
sys.stderr.write(%s: %s %s %s\n%(c.strip(),color[0], color[1], value))
return color[0], value
# Open the xpm file for reading
xpm = open(sys.argv[1])
# Read in lines until we fidn the start of the array
meta = [xpm.readline()]
while not meta[-1].startswith(static char *gromacs_xpm[]):
meta.append(xpm.readline())
# The next line will contain the dimensions of the array
dim = xpm.readline()
# There are four integers surrounded by quotes
nx, ny, nc, nb = [int(i) for i in unquote(dim).split()]
# The next dim[2] lines contain the color definitions
# Each pixel is encoded by dim[3] bytes, and a comment
# at the end of the line contains the corresponding value
colors = dict([col(xpm.readline()) for i in range(nc)])
for i in xpm:
if i.startswith(/*):
continue
j = unquote(i)
z = [colors[j[k:k+nb]] for k in range(0,nx,nb)]
sys.stdout.write( .join(z)+\n)
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2010-October/054557.html
2015-02-09 15:16 GMT+01:00 Julian julim...@gmail.com:
Dear Erik,
I have the matrix and I converted it with xpm2ps into a coloured image.
I want to compare the ligands at the same time so I would be interested
in the diagonal.
Which is the best way to get from the xpm matrix the diagonal plotted in
2d as a function of time and rmsd value?
Best regards,
Julian
Message: 5
Date: Mon, 9 Feb 2015 12:28:04 +
From: Erik Marklund erik.markl...@chem.ox.ac.uk
To: gmx-us...@gromacs.org gmx-us...@gromacs.org
Subject: Re: [gmx-users] g_rms with two trajectories
Message-ID: b783245e-bbc6-45dd-908f-cd21b2da3...@chem.ox.ac.uk
Content-Type: text/plain; charset=us-ascii
Dear Julian,
Use the -m flag.
Kind regards,
Erik
Erik Marklund, PhD
Postdoctoral Research Fellow, Fulford JRF
Department of Chemistry
Physical Theoretical Chemistry Laboratory
University of Oxford
South Parks Road
Oxford
OX1 3QZ
On 9 Feb 2015, at 12:20, Julian julim...@gmail.commailto:
julim...@gmail.com wrote:
Dear Gromacs Users,
I want to calculate the rmsd between two ligands - the system is exactly
the same, just the ligand binding conformations are different.
Therefore i want to use g_rms with the option -f2 as in the following
command:
g_rms -f trajout.trr -f2 ../2/trajout.trr -n -o
In g_rms -h it says that this generates a comparison matrix of one
trajectory versus the other but I don't get this matrix.
Only the normal rmsd.xvg but it seems as it is calculated to the
starting
snapshot and the f2-trajectory file is not considered.
Could anyone explain me how I execute this command correctly?
Thanks and best regards!
--
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[gmx-users] Insufficient disk space error
Dear Gmx User, I was running a simulation in Ubuntu 14.0 for 20 ns. I have a total disk space of 120 GB. I was running the sim from Downloads/Gromacs/build folder. But after runing 9 ns, the siom stops giving an error message insufficient disk space. I have check the space it have more than 110 GB. Please help me encounter this problem. Salam Pradeep , Tezpur University, Assam, India -- 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 and histograms smoothness
On 2/9/15 8:55 PM, Agnivo Gosai wrote: Dear Users Dr. Lemkul , thanks for the suggestions. I am using pdb2gmx for generating the topology and the itp files. Therein , automatic position restraints are generated. Now, I have never used manual restrain force constants. If you're using the pull code, yes you are. There's a force constant associated with the spring that is applying the umbrella (harmonic) potential. If that's not clear, stop everything you're doing and read every paper and book chapter you can find so you understand what you're doing rather than just typing in what a tutorial said. Could any user suggest any source / literature for choosing restraint forces for DNA/protein systems ? There is a wealth of information on umbrella sampling, steered MD, etc. Google will show you in seconds. Regarding window setup, is it the spacing of the windows ? Possibly. Except for simulation time is there any other method for increasing sampling ? Time is the primary issue here (as in most any simulation). -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] Umbrella Sampling and histograms smoothness
Dear Users Dr. Lemkul , thanks for the suggestions. I am using pdb2gmx for generating the topology and the itp files. Therein , automatic position restraints are generated. Now, I have never used manual restrain force constants. Could any user suggest any source / literature for choosing restraint forces for DNA/protein systems ? Regarding window setup, is it the spacing of the windows ? Except for simulation time is there any other method for increasing sampling ? I have read the manual but could not find anything. I am searching in the web also. Thanks Regards Agnivo Gosai Grad Student, Iowa State University. On 2/9/15 4:11 PM, Agnivo Gosai wrote: Dear Users My umbrella sampling simulations are of 1 ns time whereas Dr. Lemkul's tutorial advocates a 10 ns simulation time. I found that after running WHAM , my histograms are coarser ( rough) compared to Dr. Lemkul's. A few of my histograms have two peaks!! So should I increase the simulation time from 1 ns to 10 ns ?? I do a 100 ps NPT equilibration and then a 1 ns umbrella sampling in each of my windows. The generated PMF curve is also not smooth and is discontinuous at one position which I think I can fix by adding more windows around that co-ordinate. A picture is linked : HISTO https://docs.google.com/file/d/0B-U8uULVZjfRQXcyUkI2bXhBcVE/edit?usp=drive_web Kindly help. You need to assess convergence like you would for any type of system. Most of your peaks look rocky, so that generally indicates insufficient sampling, poor window setup, suboptimal restraint force constant, or some combination of those. Don't think that 10 ns is some magic number, either. It worked for that system after I did a bunch of checking and the result was converged. Some umbrella sampling takes way more time. -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] A question regarding electrostatic and coulomb energies.
On Mon, Feb 9, 2015 at 12:40 PM, IÑIGO SAENZ inigo.saen...@estudiant.upf.edu wrote: Dear Mark, I've been researching about energy groups and I think that it isn't the solution for my problems. The background of my question is the following: I'm currently working with the people that develops ACEMD and because of that I've got access to some information that ACEMD uses for its calculations. For each system that I simulate, I've got the list of all the pairs of atoms that must be excluded in the nonbonded calculations (e.g. atoms that are bound, 1-3 bound atoms and so on) On the other hand, I also have a list of all the pairs that must be included in the nonbonded calculations (1-n bound atoms, for n=4 and so on) grompp handles these details in response to the nrexcl setting in the .top - there's a few lines of docs in chapter 5 somewhere. The point is that I need to use that information (and more info that ACEMD provides me) to generate a .gro and .top file in order to be able to run the systems both in ACEMD and in Gromacs. When I perform a SPE of a system in both ACEMD and Gromacs, the bond, angle and dihedral energies are approximately equals in both, but Coulomb and VDW energies are very very different and this is driving me crazy. I think this has come up on the list before, perhaps even with ACEMD. Recent versions of GROMACS, particularly with the Verlet cutoff scheme, shift the potential across its whole range by the value it takes at the cutoff, so that it is the integral of the force. Not all packages do this, but you have to do it consistently if you want the comparison. Mark Hoping that you can help me, if any of you need more information about the .gro, the .top or the information that ACEMD provides me, don't hesitate in contact me. Thank you very much in advance. Iñigo S. -- 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] Cluster recommendations
Note that perf/W or perf/buck of a certain simulation on a certain hardware can be quite misleading. Currently we balance CPU-GPU load by shifting long-range electrostatics work to the short-range kernels. This involves a tradeoff which does not always give the benefit one may expect and that's because with the cut-off scaling the GPU load increases much more than the gain in total performance (and this will likely show in the power consumption too). E.g. for a 15% cut-off scaling you'll get nearly 1.5x (=1.15^3) increase in GPU work, but probably only ~5-7% performance improvement. More importantly however, with a GPU that's only 2/3s of the performance of the first one you get 10% lower performance. To put that in perspective, that's roughly the performance difference between a GTX 770 and 780 Ti. So if a GTX 770 gives a balanced run with the CPU of your choice, than using a 780 Ti may not be the most advantageous thing to do as the latter costs twice as much as the former. It is also rather difficult (and borderline unfair) to make comparisons between a less two CPUs that have very different performance (and cost) by pairing both with the same GPU! Cheers, -- Szilárd On Mon, Feb 2, 2015 at 2:11 PM, Carsten Kutzner ckut...@gwdg.de wrote: Hi David, On 22 Jan 2015, at 18:01, David McGiven davidmcgiv...@gmail.com wrote: Hey Karsten, Just another question. What do you think will be the performance difference between two gromacs runs with a ~100k atoms system like the one I mentioned on my first email : - 1 server with 4 AMD processors, 16 cores each (64 cores) with no GPU - 1 server with 4 AMD processors, 16 cores each (64 cores) with one GTX 980 GPU - 1 server with 2 Intel processors, 10 cores each (20 cores) like the ones you mentioned, with one or two GTX 980 GPU. I'm not interested in exact performance numbers, I just need to understand the logistics behind the CPU/GPU combinations in order to make an inteligent cluster purchase. I never benchmarked 64-core AMD nodes with GPUs. With a 80 k atoms test system using a 2 fs time step I get 24 ns/d on 64 AMD cores 6272 16 ns/d on 32 AMD cores 6380 36 ns/d on 32 AMD cores 6380 with 1x GTX 980 40 ns/d on 32 AMD cores 6380 with 2x GTX 980 27 ns/d on 20 Intel cores 2680v2 52 ns/d on 20 Intel cores 2680v2 with 1x GTX 980 62 ns/d on 20 Intel cores 2680v2 with 2x GTX 980 So unless you can get the AMD nodes very cheap, probably the 20-core Intel nodes with 1 or 2 GPUs will give you the best performance and the best performance/price. Best, Carsten Thanks again. Best, D 2015-01-16 14:46 GMT+01:00 Carsten Kutzner ckut...@gwdg.de: Hi David, On 16 Jan 2015, at 12:28, David McGiven davidmcgiv...@gmail.com wrote: Hi Carsten, Thanks for your answer. 2015-01-16 11:11 GMT+01:00 Carsten Kutzner ckut...@gwdg.de: Hi David, we are just finishing an evaluation to find out which is the optimal hardware for Gromacs setups. One of the input systems is an 80,000 atom membrane channel system and thus nearly exactly what you want to compute. The biggest benefit you will get by adding one or two consumer-class GPUs to your nodes (e.g. NVIDIA GTX 980). That will typically double your performace-to-price ratio. This is true for Intel as well as for AMD nodes, however the best ratio in our tests was observed with 10-core Intel CPUs (2670v2, 2680v2) in combination with a GTX 780Ti or 980, ideally two of those CPUs with two GPUs on a node. Was there a difference between 2670v2 (2.5 GHz) and 2680v2 (2.8 GHz) ? I'm wondering if those 0,3 GHz are significative. Or the 0,5 GHz compared to 2690v2 for the matter. There’s a significative difference in price indeed. Usually the percent improvement for Gromacs performance is not as much as the percent improvement in clock speed, so the cheaper ones will give you a higher performance-to-price ratio. I'm also wondering if the performance would be better with 16 core Intels instead of 10 core. I.e E5-2698 v3. Didn’t test those. I would like to know which other tests have you done. What about AMD ? We tested AMD 6380 with 1-2 GTX 980 GPUs, which gives about the same performance-to-price ratio as a 10 core Intel 2680v2 node with one GTX 980. The Intel node gives you a higher per-node performance, though. Unless you want to buy expensive FDR14 Infiniband, scaling across two or more of those nodes won’t be good (~0.65 parallel efficiency across 2, ~0.45 across 4 nodes using QDR infiniband), so I would advise against it and go for more sampling on single nodes. Well, that puzzles me. Why is it that you get poor performance ? Are you talking about pure CPU jobs over infiniband, or are you talking about CPU+GPU jobs over infiniband ? For a given network (e.g. QDR Infiniband), the scaling is better the lower the performance of the individual nodes. So for CPU-only nodes you will get a better scaling than for CPU+GPU nodes, which have a
Re: [gmx-users] Umbrella Sampling and histograms smoothness
On 2/9/15 4:11 PM, Agnivo Gosai wrote: Dear Users My umbrella sampling simulations are of 1 ns time whereas Dr. Lemkul's tutorial advocates a 10 ns simulation time. I found that after running WHAM , my histograms are coarser ( rough) compared to Dr. Lemkul's. A few of my histograms have two peaks!! So should I increase the simulation time from 1 ns to 10 ns ?? I do a 100 ps NPT equilibration and then a 1 ns umbrella sampling in each of my windows. The generated PMF curve is also not smooth and is discontinuous at one position which I think I can fix by adding more windows around that co-ordinate. A picture is linked : HISTO https://docs.google.com/file/d/0B-U8uULVZjfRQXcyUkI2bXhBcVE/edit?usp=drive_web Kindly help. You need to assess convergence like you would for any type of system. Most of your peaks look rocky, so that generally indicates insufficient sampling, poor window setup, suboptimal restraint force constant, or some combination of those. Don't think that 10 ns is some magic number, either. It worked for that system after I did a bunch of checking and the result was converged. Some umbrella sampling takes way more time. -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] Query regarding gaps between lipid molecules in a heterogenous system of 1464 dopc and dopg
On 2/9/15 11:00 AM, Agnivo Gosai wrote: Hi Antara Did you check the plot of the potential energy against the simulation time ? You can visualize the convergence of your energy minimisation from the above plot. Energy minimization, by definition, converges to some value (but there is no time in EM, it's not a dynamical process). That converged result is what is printed. There's usually nothing informative when EM converges without complaint. -Justin Thanks Regards Agnivo Gosai Grad Student, Iowa State University. On 2/9/15 7:41 AM, Antara mazumdar wrote: i got the following result after EM of this system of mine. writing lowest energy coordinates. Steepest Descents converged to Fmax 1000 in 15280 steps Potential Energy = -5.0853170e+06 Maximum force = 9.9438867e+02 on atom 179440 Norm of force = 7.8095098e+00 Should i go ahead with NVT and NPT? -- Is there a reason you think you shouldn't? What outcome do you expect? Does this outcome meet that expectation? Does the structure look sensible? -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] Umbrella Sampling and histograms smoothness
Dear Users My umbrella sampling simulations are of 1 ns time whereas Dr. Lemkul's tutorial advocates a 10 ns simulation time. I found that after running WHAM , my histograms are coarser ( rough) compared to Dr. Lemkul's. A few of my histograms have two peaks!! So should I increase the simulation time from 1 ns to 10 ns ?? I do a 100 ps NPT equilibration and then a 1 ns umbrella sampling in each of my windows. The generated PMF curve is also not smooth and is discontinuous at one position which I think I can fix by adding more windows around that co-ordinate. A picture is linked : HISTO https://docs.google.com/file/d/0B-U8uULVZjfRQXcyUkI2bXhBcVE/edit?usp=drive_web Kindly help. Thanks Regards Agnivo Gosai Grad Student, Iowa State University. -- 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] Query regarding generation of gaps between lipid molecules after minimisation even after using position restraints
Hi, I minimised a heterogenous lipid system of 1464 DOPC and DOPG and applied position restraints as well as had vdwradii.dat file for genbox step. Yet after minimisation, there are gaps between the lipid molecules. Pls suggest a remedy. -- Regards, Antara -- J.R.F.(Project) Systems Biology Group CSIR - Institute of Genomics Integrative Biology South Campus, New Delhi-110020 M:+91-9717970040 -- -- 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] A question regarding electrostatic and coulomb energies.
Dear Mark, I've been researching about energy groups and I think that it isn't the solution for my problems. The background of my question is the following: I'm currently working with the people that develops ACEMD and because of that I've got access to some information that ACEMD uses for its calculations. For each system that I simulate, I've got the list of all the pairs of atoms that must be excluded in the nonbonded calculations (e.g. atoms that are bound, 1-3 bound atoms and so on) On the other hand, I also have a list of all the pairs that must be included in the nonbonded calculations (1-n bound atoms, for n=4 and so on) The point is that I need to use that information (and more info that ACEMD provides me) to generate a .gro and .top file in order to be able to run the systems both in ACEMD and in Gromacs. When I perform a SPE of a system in both ACEMD and Gromacs, the bond, angle and dihedral energies are approximately equals in both, but Coulomb and VDW energies are very very different and this is driving me crazy. Hoping that you can help me, if any of you need more information about the .gro, the .top or the information that ACEMD provides me, don't hesitate in contact me. Thank you very much in advance. Iñigo S. -- 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] g_rms with two trajectories
Dear Erik, I have the matrix and I converted it with xpm2ps into a coloured image. I want to compare the ligands at the same time so I would be interested in the diagonal. Which is the best way to get from the xpm matrix the diagonal plotted in 2d as a function of time and rmsd value? Best regards, Julian Message: 5 Date: Mon, 9 Feb 2015 12:28:04 + From: Erik Marklund erik.markl...@chem.ox.ac.uk To: gmx-us...@gromacs.org gmx-us...@gromacs.org Subject: Re: [gmx-users] g_rms with two trajectories Message-ID: b783245e-bbc6-45dd-908f-cd21b2da3...@chem.ox.ac.uk Content-Type: text/plain; charset=us-ascii Dear Julian, Use the -m flag. Kind regards, Erik Erik Marklund, PhD Postdoctoral Research Fellow, Fulford JRF Department of Chemistry Physical Theoretical Chemistry Laboratory University of Oxford South Parks Road Oxford OX1 3QZ On 9 Feb 2015, at 12:20, Julian julim...@gmail.commailto: julim...@gmail.com wrote: Dear Gromacs Users, I want to calculate the rmsd between two ligands - the system is exactly the same, just the ligand binding conformations are different. Therefore i want to use g_rms with the option -f2 as in the following command: g_rms -f trajout.trr -f2 ../2/trajout.trr -n -o In g_rms -h it says that this generates a comparison matrix of one trajectory versus the other but I don't get this matrix. Only the normal rmsd.xvg but it seems as it is calculated to the starting snapshot and the f2-trajectory file is not considered. Could anyone explain me how I execute this command correctly? Thanks and best regards! -- 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.orgmailto: 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] g_rms with two trajectories
Dear Gromacs Users, I want to calculate the rmsd between two ligands - the system is exactly the same, just the ligand binding conformations are different. Therefore i want to use g_rms with the option -f2 as in the following command: g_rms -f trajout.trr -f2 ../2/trajout.trr -n -o In g_rms -h it says that this generates a comparison matrix of one trajectory versus the other but I don't get this matrix. Only the normal rmsd.xvg but it seems as it is calculated to the starting snapshot and the f2-trajectory file is not considered. Could anyone explain me how I execute this command correctly? Thanks and best regards! -- 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 Samling Alteration
On 2/8/15 5:53 PM, Alexander Law wrote: This method doesn't work. Does each simulation have to complete the 10 ns in order to move on the analysis step, or can I use incomplete simulations? Analyze however much time you like. If not, is there another possibility to force the simulations to complete? If by complete you mean terminate ahead of schedule that's what Ctrl+C or whatever queue commands (e.g. qdel) are for. -Justin Thanks, Alex 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: Friday, February 06, 2015 12:07 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Umbrella Samling Alteration On 2/4/15 7:22 PM, Alexander Law wrote: Hi Justin The runs have started but they are not currently running, as in they were cancelled and I can start them up again using the .cpt file. Is it still possible to alter add the -nsteps in this case? That should always be possible. Try it and see. -Justin Many Thanks, Alex 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: Tuesday, February 03, 2015 1:51 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Umbrella Samling Alteration On 2/1/15 11:22 PM, Alexander Law wrote: Dear Gromacs Users I am currently running the series of simulations using the following command: mdrun -deffnm umbrella0 -pf pullf-umbrella0.xvg -px pullx-umbrella0.xvg I wish to lessen the amount of time for each of these simulations from 10 ns to 6 ns. These simulations are already up to around 5 ns, is it possible to change the time to 6 ns without altering the md_umbrella.mdp file and starting agin? Also, will this reduction have any major impacts on the quality/efficacy of the data? Use mdrun command-line option -nsteps to override the number of steps specified in the .tpr file, but you can't do this if the runs are in progress. -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. This email may be confidential and subject to legal privilege, it may not reflect the views of the University of Canterbury, and it is not guaranteed to be virus free. If you are not an intended recipient, please notify the sender immediately and erase all copies of the message and any attachments. Please refer to http://www.canterbury.ac.nz/emaildisclaimer for more information. -- == 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. This email may be confidential and subject to legal privilege, it may not reflect the views of the University of Canterbury, and it is not guaranteed to be virus free. If you are not an intended recipient, please notify the sender immediately and erase all copies of the message and any attachments. Please refer to http://www.canterbury.ac.nz/emaildisclaimer for more information. -- == 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
Re: [gmx-users] ERROR OBTAINED FOR NVT OF DOPC AND PROTEIN SIMULATIONS
On 2/9/15 7:34 AM, Antara mazumdar wrote: eRROR OBTAINED DURING NVT: Water molecule starting at atom 673675 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. NVT CONDITIONS WERE : n for B2AR-POPC system define = -DPOSRES ; Protein is position restrained (uses the posres.itp file information) ; Parameters describing the details of the NVT simulation protocol integrator = md; Algorithm (md = molecular dynamics [leap-frog integrator]; md-vv = md using velocity verlet; sd = stochastic dynamics) dt = 0.002 ; Time-step (ps) nsteps = 25; Number of steps to run (0.002 * 25 = 500 ps) ; Parameters controlling output writing nstxout = 1000 ; Write coordinates to output .trr file every 2 ps nstvout = 1000 ; Write velocities to output .trr file every 2 ps nstenergy = 1000 ; Write energies to output .edr file every 2 ps nstlog = 1000 ; Write output to .log file every 2 ps ; Parameters describing neighbors searching and details about interaction calculations ns_type = grid ; Neighbor list search method (simple, grid) nstlist = 5 ; Neighbor list update frequency (after every given number of steps) rlist = 1.2 ; Neighbor list search cut-off distance (nm) rcoulomb= 1.2 ; Short-range Coulombic interactions cut-off distance (nm) rvdw= 1.2 ; Short-range van der Waals cutoff distance (nm) pbc = xyz ; Direction in which to use Perodic Boundary Conditions (xyz, xy, no) ; Parameters for treating bonded interactions continuation= no; Whether a fresh start or a continuation from a previous run (yes/no) constraint_algorithm = LINCS; Constraint algorithm (LINCS / SHAKE) constraints = all-bonds ; Which bonds/angles to constrain (all-bonds / hbonds / none / all-angles / h-angles) lincs_iter = 2 ; Number of iterations to correct for rotational lengthening in LINCS (related to accuracy) lincs_order = 8 ; Highest order in the expansion of the constraint coupling matrix (related to accuracy) ; Parameters for treating electrostatic interactions coulombtype = PME ; Long range electrostatic interactions treatment (cut-off, Ewald, PME) pme_order = 4 ; Interpolation order for PME (cubic interpolation is represented by 4) fourierspacing = 0.16 ; Maximum grid spacing for FFT grid using PME (nm) ; Temperature coupling parameters tcoupl = V-rescale ; Modified Berendsen thermostat using velocity rescaling tc-grps = Protein DOPC SOL_NA ; Define groups to be coupled separately to temperature bath tau_t = 0.1 0.1 0.1 ; Group-wise coupling time constant (ps) ref_t = 300 300 300 ; Group-wise reference temperature (K) ; Pressure coupling parameters pcoupl = no; Under NVT conditions pressure coupling is not done http://www.gromacs.org/Documentation/Terminology/Blowing_Up Google will turn up about 27 million posts with the same problem. Please investigate the list archive (that's why it's there). -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] pH during free energy calculation
Dear Experts and users, I am running simulation for solvation free energy calculation using thermodynamic integration approach (as mentioned in Justin's tutorial). My system consist of a cation molecule, an anion molecule and bulk of solvent molecules. I want to understand the pH of my system, what will be the default pH for such a system? It will be helpful if anybody can comment on such a simulation and help in understanding pH behavior of such systems? Waiting for useful comments and insights from the community. regards, Vivek -- 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] Query regarding gaps between lipid molecules in a heterogenous system of 1464 dopc and dopg
On 2/9/15 7:41 AM, Antara mazumdar wrote: i got the following result after EM of this system of mine. writing lowest energy coordinates. Steepest Descents converged to Fmax 1000 in 15280 steps Potential Energy = -5.0853170e+06 Maximum force = 9.9438867e+02 on atom 179440 Norm of force = 7.8095098e+00 Should i go ahead with NVT and NPT? -- Is there a reason you think you shouldn't? What outcome do you expect? Does this outcome meet that expectation? Does the structure look sensible? -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] ERROR OBTAINED FOR NVT OF DOPC AND PROTEIN SIMULATIONS
eRROR OBTAINED DURING NVT: Water molecule starting at atom 673675 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. NVT CONDITIONS WERE : n for B2AR-POPC system define = -DPOSRES ; Protein is position restrained (uses the posres.itp file information) ; Parameters describing the details of the NVT simulation protocol integrator = md; Algorithm (md = molecular dynamics [leap-frog integrator]; md-vv = md using velocity verlet; sd = stochastic dynamics) dt = 0.002 ; Time-step (ps) nsteps = 25; Number of steps to run (0.002 * 25 = 500 ps) ; Parameters controlling output writing nstxout = 1000 ; Write coordinates to output .trr file every 2 ps nstvout = 1000 ; Write velocities to output .trr file every 2 ps nstenergy = 1000 ; Write energies to output .edr file every 2 ps nstlog = 1000 ; Write output to .log file every 2 ps ; Parameters describing neighbors searching and details about interaction calculations ns_type = grid ; Neighbor list search method (simple, grid) nstlist = 5 ; Neighbor list update frequency (after every given number of steps) rlist = 1.2 ; Neighbor list search cut-off distance (nm) rcoulomb= 1.2 ; Short-range Coulombic interactions cut-off distance (nm) rvdw= 1.2 ; Short-range van der Waals cutoff distance (nm) pbc = xyz ; Direction in which to use Perodic Boundary Conditions (xyz, xy, no) ; Parameters for treating bonded interactions continuation= no; Whether a fresh start or a continuation from a previous run (yes/no) constraint_algorithm = LINCS; Constraint algorithm (LINCS / SHAKE) constraints = all-bonds ; Which bonds/angles to constrain (all-bonds / hbonds / none / all-angles / h-angles) lincs_iter = 2 ; Number of iterations to correct for rotational lengthening in LINCS (related to accuracy) lincs_order = 8 ; Highest order in the expansion of the constraint coupling matrix (related to accuracy) ; Parameters for treating electrostatic interactions coulombtype = PME ; Long range electrostatic interactions treatment (cut-off, Ewald, PME) pme_order = 4 ; Interpolation order for PME (cubic interpolation is represented by 4) fourierspacing = 0.16 ; Maximum grid spacing for FFT grid using PME (nm) ; Temperature coupling parameters tcoupl = V-rescale ; Modified Berendsen thermostat using velocity rescaling tc-grps = Protein DOPC SOL_NA ; Define groups to be coupled separately to temperature bath tau_t = 0.1 0.1 0.1 ; Group-wise coupling time constant (ps) ref_t = 300 300 300 ; Group-wise reference temperature (K) ; Pressure coupling parameters pcoupl = no; Under NVT conditions pressure coupling is not done -- Regards, Antara -- J.R.F.(Project) Systems Biology Group CSIR - Institute of Genomics Integrative Biology South Campus, New Delhi-110020 M:+91-9717970040 -- -- 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] Query regarding gaps between lipid molecules in a heterogenous system of 1464 dopc and dopg
i got the following result after EM of this system of mine. writing lowest energy coordinates. Steepest Descents converged to Fmax 1000 in 15280 steps Potential Energy = -5.0853170e+06 Maximum force = 9.9438867e+02 on atom 179440 Norm of force = 7.8095098e+00 Should i go ahead with NVT and NPT? -- Regards, Antara -- J.R.F.(Project) Systems Biology Group CSIR - Institute of Genomics Integrative Biology South Campus, New Delhi-110020 M:+91-9717970040 -- -- 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] H-Bonding residues against specific frames
On 2/8/15 6:08 PM, Agnivo Gosai wrote: Dear Users I am using g_hbond to get the H-bonds for a particular simulation over the entire trajectory. In the log file I can find which reesidues are forming H-bonds. However , I want the H-bonds formed over the entire simulation length frame wise or for a particular frame. How can I do so ? I was thinking of extracting every frame (using trjconv) from my total of 501 frames and running g_hbond on each of the frames. But that seems to be a laborious process. Is there any way out ? Use -hbm -hbn to write an H-bond existence matrix, and use the index file created by -hbn to map out which ones are which. -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] Query regarding generation of gaps between lipid molecules after minimisation even after using position restraints
On 2/9/15 5:07 AM, Antara mazumdar wrote: Hi, I minimised a heterogenous lipid system of 1464 DOPC and DOPG and applied position restraints as well as had vdwradii.dat file for genbox step. Yet after minimisation, there are gaps between the lipid molecules. Pls suggest a remedy. Equilibrate thoroughly. -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] g_rms with two trajectories
Dear Julian, Use the -m flag. Kind regards, Erik Erik Marklund, PhD Postdoctoral Research Fellow, Fulford JRF Department of Chemistry Physical Theoretical Chemistry Laboratory University of Oxford South Parks Road Oxford OX1 3QZ On 9 Feb 2015, at 12:20, Julian julim...@gmail.commailto:julim...@gmail.com wrote: Dear Gromacs Users, I want to calculate the rmsd between two ligands - the system is exactly the same, just the ligand binding conformations are different. Therefore i want to use g_rms with the option -f2 as in the following command: g_rms -f trajout.trr -f2 ../2/trajout.trr -n -o In g_rms -h it says that this generates a comparison matrix of one trajectory versus the other but I don't get this matrix. Only the normal rmsd.xvg but it seems as it is calculated to the starting snapshot and the f2-trajectory file is not considered. Could anyone explain me how I execute this command correctly? Thanks and best regards! -- 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.orgmailto: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] pH during free energy calculation
On 2/9/15 7:42 AM, vivek sharma wrote: Dear Experts and users, I am running simulation for solvation free energy calculation using thermodynamic integration approach (as mentioned in Justin's tutorial). My system consist of a cation molecule, an anion molecule and bulk of solvent molecules. I want to understand the pH of my system, what will be the default pH for such a system? It will be helpful if anybody can comment on such a simulation and help in understanding pH behavior of such systems? Waiting for useful comments and insights from the community. There are no exchangeable protons in a classical MD simulation, so there is no pH. There are constant pH simulations, but those are fundamentally different. See the numerous discussions on this topic in the archive. -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] g_rms with two trajectories
Dear Julian, I see no other means than writing a script to parse out the diagonal. The xpm format is quite human readable so I don’t think it will take you long to figure out how to do. Kind regards, Erik On 9 Feb 2015, at 14:16, Julian julim...@gmail.commailto:julim...@gmail.com wrote: Dear Erik, I have the matrix and I converted it with xpm2ps into a coloured image. I want to compare the ligands at the same time so I would be interested in the diagonal. Which is the best way to get from the xpm matrix the diagonal plotted in 2d as a function of time and rmsd value? Best regards, Julian Message: 5 Date: Mon, 9 Feb 2015 12:28:04 + From: Erik Marklund erik.markl...@chem.ox.ac.ukmailto:erik.markl...@chem.ox.ac.uk To: gmx-us...@gromacs.orgmailto:gmx-us...@gromacs.org gmx-us...@gromacs.orgmailto:gmx-us...@gromacs.org Subject: Re: [gmx-users] g_rms with two trajectories Message-ID: b783245e-bbc6-45dd-908f-cd21b2da3...@chem.ox.ac.ukmailto:b783245e-bbc6-45dd-908f-cd21b2da3...@chem.ox.ac.uk Content-Type: text/plain; charset=us-ascii Dear Julian, Use the -m flag. Kind regards, Erik Erik Marklund, PhD Postdoctoral Research Fellow, Fulford JRF Department of Chemistry Physical Theoretical Chemistry Laboratory University of Oxford South Parks Road Oxford OX1 3QZ On 9 Feb 2015, at 12:20, Julian julim...@gmail.commailto:julim...@gmail.commailto: julim...@gmail.commailto:julim...@gmail.com wrote: Dear Gromacs Users, I want to calculate the rmsd between two ligands - the system is exactly the same, just the ligand binding conformations are different. Therefore i want to use g_rms with the option -f2 as in the following command: g_rms -f trajout.trr -f2 ../2/trajout.trr -n -o In g_rms -h it says that this generates a comparison matrix of one trajectory versus the other but I don't get this matrix. Only the normal rmsd.xvg but it seems as it is calculated to the starting snapshot and the f2-trajectory file is not considered. Could anyone explain me how I execute this command correctly? Thanks and best regards! -- 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.orgmailto:gmx-users-requ...@gromacs.orgmailto: gmx-users-requ...@gromacs.orgmailto: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.orgmailto: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] g_rms with two trajectories
Juilan,
A quick way to do this is with an awk script, such as:
awk '{print $NR}' (your matrix.dat file here). This will print the diagonal of
the matrix. If you want the one from the .xpm file you need to use something
like:
awk '{if($0!~/*/){print substr($0,counter+2,1),counter++}}' Though the output
will be letters that correspond to different rmsd values (as shown at the top
of the .xpm file) which will require you to modify this script more to include
a look-up to get back the number values (hence why using the matrix.dat file
may be easier).
Kind Regards,
Micholas
===
Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Julian
julim...@gmail.com
Sent: Monday, February 09, 2015 9:16 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] g_rms with two trajectories
Dear Erik,
I have the matrix and I converted it with xpm2ps into a coloured image.
I want to compare the ligands at the same time so I would be interested
in the diagonal.
Which is the best way to get from the xpm matrix the diagonal plotted in 2d
as a function of time and rmsd value?
Best regards,
Julian
Message: 5
Date: Mon, 9 Feb 2015 12:28:04 +
From: Erik Marklund erik.markl...@chem.ox.ac.uk
To: gmx-us...@gromacs.org gmx-us...@gromacs.org
Subject: Re: [gmx-users] g_rms with two trajectories
Message-ID: b783245e-bbc6-45dd-908f-cd21b2da3...@chem.ox.ac.uk
Content-Type: text/plain; charset=us-ascii
Dear Julian,
Use the -m flag.
Kind regards,
Erik
Erik Marklund, PhD
Postdoctoral Research Fellow, Fulford JRF
Department of Chemistry
Physical Theoretical Chemistry Laboratory
University of Oxford
South Parks Road
Oxford
OX1 3QZ
On 9 Feb 2015, at 12:20, Julian julim...@gmail.commailto:
julim...@gmail.com wrote:
Dear Gromacs Users,
I want to calculate the rmsd between two ligands - the system is exactly
the same, just the ligand binding conformations are different.
Therefore i want to use g_rms with the option -f2 as in the following
command:
g_rms -f trajout.trr -f2 ../2/trajout.trr -n -o
In g_rms -h it says that this generates a comparison matrix of one
trajectory versus the other but I don't get this matrix.
Only the normal rmsd.xvg but it seems as it is calculated to the starting
snapshot and the f2-trajectory file is not considered.
Could anyone explain me how I execute this command correctly?
Thanks and best regards!
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