[gmx-users] REST2 with gromacs-4.5.5 plumed2.2.0 -hrex
Hi All, I am running into a few problems trying to do REST2 using the version of plumed available at github.com/GiovanniBussi/plumed2/tree/v2.0-hrex. I have successfully patched gromacs-4.5.5 with plumed downloaded from the link and when I run mdrun_mpi -h the -plumed option is properly displayed. Later I prepared a simulation with a small protein marking all of the protein atoms as hot atoms ( with _ tag ) in the processed.top file. The temperature range selected was from 300 to 500 and I used the script mentioned in hrex.txt for generating topol$i.top files for 8 replicas. At this point, I was confused as to how the .mdp files for the different replicas should contain. When I kept the temperature for all the replicas at 300 (Assuming that temperature is taken care by lambda scaling of the parameters in the .top files). I ran mdrun_mpi with the -hrex flag but it returns me the following exchange probability Replica exchange at step 250 time 0.5 dplumed = 0.000e+00 d = 0.000e+00Repl 0 - 1 dE = 0.000e+00 dpV = 0.000e+00 d = 0.000e+00 Repl ex 0 x 12 x 34 x 56 x 7 Repl pr 1.0 1.0 1.0 1.0 Looks like the replica exchange probability is taken as 1.0. Is it because all the temperatures are the same in the .mdp files? It doesnt return any error message regarding this as well. Please help me identify the problem. regards, Saravanan -- Saravanan Murugeson Graduate Student Lab-2, Department of Biological sciences and Bio-engineering, Indian Institute of Technology Kanpur 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.
[gmx-users] how to split gromacs tpr file
Hi everyone, i have successfully ran 10ns antigen-antibody simulation job . its generates huge data. i want to make movie of it by using chimera but my computer energy is not enough to open such a huge data on chimera and it get hang. kindly anybody tell me how i can make movie of it or otherwise how i can split .tpr file so i can make of it . -- With best regards, SIDRA RAFI, Jr.Research Fellow,P-103 Email: sidraraf...@gmail.com, sidra.r...@iccs.edu Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi www.iccs.edu/pcmd/index.php -- 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] how to split gromacs tpr file
Depends what the origin of the problem is... see http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume Mark On Thu, Mar 6, 2014 at 12:21 PM, sidra rafi sidraraf...@gmail.com wrote: Hi everyone, i have successfully ran 10ns antigen-antibody simulation job . its generates huge data. i want to make movie of it by using chimera but my computer energy is not enough to open such a huge data on chimera and it get hang. kindly anybody tell me how i can make movie of it or otherwise how i can split .tpr file so i can make of it . -- With best regards, SIDRA RAFI, Jr.Research Fellow,P-103 Email: sidraraf...@gmail.com, sidra.r...@iccs.edu Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi www.iccs.edu/pcmd/index.php -- 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] Generate many random configurations
I have figured out to accomplish what I want by writing a bash script. However, one thing I am still struggling with is determining how to concatenate the resulting configurations. There are two possible solutions: 1) concatenate multiple .gro files that have been generated at the end or 2) concatenate after each iteration. I like the idea of the second option. Does anyone have any suggestions as to how to do this? Thanks, Blake -- View this message in context: http://gromacs.5086.x6.nabble.com/Generate-many-random-configurations-tp5014976p5014993.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Fwd: sigma unit conversion
The Amber molecular dynamics program (sander) uses a different format of the van der Waals equation, so Amber force fields are designed to use different parameters than those used in Gromacs. So, it's not as simple as converting from Angstroms to nanometers. The coefficents used in the Amber force fields are not simply Gromacs sigma and epsilon. Here is a document related to your question from the Amber site: http://ambermd.org/Questions/vdwequation.pdf Additionally combination rule 2 in Gromacs is a Lorentz-Berthelot rule (see section 5.3.2 in the Gromacs manual). This is just how the force field was designed. I'm just someone who uses acpype occasionally, so I hope this is helpful. James Barnett On Wed, Mar 05, 2014 at 10:17:27PM -0600, Chetan Mahajan wrote: Hi all, I am using Amber2gromacs tool called as acpype for converting input files to Amber to input files for gromacs. I have a question regarding atomtypes section of .top file. Here are first two rows of that section in my file: name bond_type mass charge ptype sigma epsilon Amb Ti Ti0.0 0.0A 1.39461e-01 6.08772e-02 ; 0.78 0.0145 OT OT0.0 0.0A 2.87832e-01 8.29687e-02 ; 1.62 0.0198 Now, in my .top file, each row contains, at the end, Amber force field values for sigma and epsilon are given. Values on the left indicate unit converted values. However, given that Amber units are A0 for sigma, converted value for gromacs, which should be in nanometer does not match. Combination rule chosen is 2. ( by the way, how is this rule chosen ?) Thanks Chetan -- 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] Generate many random configurations
Thanks for your reply and helpful suggestions Justin. I have successfully implemented the concatenation command (after generating the desired number of configurations). There is another detail with which I am having trouble. So, I actually want to generate configurations in which it is possible for atoms to overlap, as in an ideal gas. To do that, I set vdwd to 0.01 nm and used atom names that are not contained in the vdwradii.dat file so that vdwd will actually be used. (Ideally, I want to use vdwd=0, but I receive the error, One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than the cut-off.). Regardless, even when vdwd=0.01, the g(r) still equals 0 at distances = 0.1 nm. Do you have any ideas why this is the case? I thought that the g(r) would be equal to zero at distances = 0.01 nm. Thanks, Blake -- View this message in context: http://gromacs.5086.x6.nabble.com/Generate-many-random-configurations-tp5014976p5014997.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] ParamChem CHARMM to GROMACS conversion
Hi All, I am pleased to announce the immediate availability of a script to convert a CHARMM stream (.str) file to GROMACS .itp format as part of an effort to better interface the ParamChem server (www.paramchem.org) and CHARMM force field with GROMACS. You will now be able to parametrize a small molecule using ParamChem and the latest CGenFF force field (version 2b8) and run the simulation in GROMACS using our latest CHARMM36 force field release from January. You can get both the conversion script (written in Python) and the CHARMM36/CGenFF 2b8 force field files from our lab's website: http://mackerell.umaryland.edu/CHARMM_ff_params.html Please read the header of the conversion script for a usage guide and contact information in case of problems or questions. Enjoy! -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.
Re: [gmx-users] Generate many random configurations
On 3/6/14, 9:50 AM, rankinb wrote: Thanks for your reply and helpful suggestions Justin. I have successfully implemented the concatenation command (after generating the desired number of configurations). There is another detail with which I am having trouble. So, I actually want to generate configurations in which it is possible for atoms to overlap, as in an ideal gas. To do that, I set vdwd to 0.01 nm and used atom names that are not contained in the vdwradii.dat file so that vdwd will actually be used. (Ideally, I want to use vdwd=0, but I receive the error, One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than the cut-off.). Regardless, even when vdwd=0.01, the g(r) still equals 0 at distances = 0.1 nm. Do you have any ideas why this is the case? I thought that the g(r) would be equal to zero at distances = 0.01 nm. Are you calculating the g(r) for a single configuration, or over a trajectory? -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.
Re: [gmx-users] Generate many random configurations
I am generating x number of random configurations by iteratively calling the
genbox command (implemented with a bash script), concatenating the results
to obtain multiple random configurations, and calculating the g(r) over all
configurations. So in a sense, I am calculating the g(r) over a trajectory,
but the trajectory was not obtained from a simulation. Here is the bash
script that I am using to do that:
#! /bin/bash
#define number of molecules to add
nmolecules=1
#define box length
boxl=1.50356
for i in {1..1}
do
rn=$i
genbox -cp coordinates_i.gro -nmol $nmolecules -ci
coordinates_i.gro -box
$boxl $boxl $boxl -vdwd 0.01 -seed $rn -o coordinates_out$i.gro
done
cat tba*.gro all.gro
As I said before, I would like to set vdwd to zero but am receiving an
error.
Thanks,
Blake
--
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Re: [gmx-users] Generate many random configurations
On 3/6/14, 3:05 PM, rankinb wrote:
I am generating x number of random configurations by iteratively calling the
genbox command (implemented with a bash script), concatenating the results
to obtain multiple random configurations, and calculating the g(r) over all
configurations. So in a sense, I am calculating the g(r) over a trajectory,
but the trajectory was not obtained from a simulation. Here is the bash
script that I am using to do that:
#! /bin/bash
#define number of molecules to add
nmolecules=1
#define box length
boxl=1.50356
for i in {1..1}
do
rn=$i
genbox -cp coordinates_i.gro -nmol $nmolecules -ci
coordinates_i.gro -box
$boxl $boxl $boxl -vdwd 0.01 -seed $rn -o coordinates_out$i.gro
done
cat tba*.gro all.gro
As I said before, I would like to set vdwd to zero but am receiving an
error.
Do you know that any of your particles are actually that close? What is the
input configuration to which you are adding your molecules? You mentioned
something before about an ideal gas, so are you just trying to add random
particles throughout some void space? I'll admit that I don't understand why
anyone would want their particles to be on top of one another, that just sounds
like a recipe for an unphysical disaster :) Perhaps you can explain a bit more
thoroughly what you're trying to do. Keep in mind that the use of -vdwd does
not guarantee that any particles will necessarily come very close, it just makes
it more likely. The neighbor searching algorithm crashes with -vdwd 0, so you
will not be able to do that.
-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
==
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[gmx-users] impropers in Gromacs and acepype tool
Hi I just wanted to check the order of atoms in a improper in gromacs input file *.top. According to urea example on page 137 ( section 5.7)of manual 4.6.4, order of i,j,k,l atoms in improper always starts with central atom, whereas that in a *.top file generated with acepype lists i,j,k,l order for improper in formate ion as H O C O. Central atom at third position. Is this right or bug in the tool acepype? I appreciate your response. Thanks Chetan -- 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] impropers in Gromacs and acepype tool
Thanks, Justin. I do not have AMBER parameter set or .rtp file. I have just one .top file which contains topologies and parameters. Just curious: where to get Amber parameter set from? On Thu, Mar 6, 2014 at 4:25 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/6/14, 5:16 PM, Chetan Mahajan wrote: Hi I just wanted to check the order of atoms in a improper in gromacs input file *.top. According to urea example on page 137 ( section 5.7)of manual 4.6.4, order of i,j,k,l atoms in improper always starts with central atom, whereas that in a *.top file generated with acepype lists i,j,k,l order for improper in formate ion as H O C O. Central atom at third position. Is this right or bug in the tool acepype? It's right. The example in the manual is for Gromos force fields. You should look at the actual .rtp files for the AMBER parameter set you're trying to use. Suffice it to say that different atom orders are supported, because the Gromacs machinery (specifically pdb2gmx) knows how to deal with lots of stuff based on bonded geometry. -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.
Re: [gmx-users] impropers in Gromacs and acepype tool
I think acepype Amber2gromacs tool has amber parameter files. but here is no .rtp On Thu, Mar 6, 2014 at 4:40 PM, Chetan Mahajan chetanv...@gmail.com wrote: Thanks, Justin. I do not have AMBER parameter set or .rtp file. I have just one .top file which contains topologies and parameters. Just curious: where to get Amber parameter set from? On Thu, Mar 6, 2014 at 4:25 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/6/14, 5:16 PM, Chetan Mahajan wrote: Hi I just wanted to check the order of atoms in a improper in gromacs input file *.top. According to urea example on page 137 ( section 5.7)of manual 4.6.4, order of i,j,k,l atoms in improper always starts with central atom, whereas that in a *.top file generated with acepype lists i,j,k,l order for improper in formate ion as H O C O. Central atom at third position. Is this right or bug in the tool acepype? It's right. The example in the manual is for Gromos force fields. You should look at the actual .rtp files for the AMBER parameter set you're trying to use. Suffice it to say that different atom orders are supported, because the Gromacs machinery (specifically pdb2gmx) knows how to deal with lots of stuff based on bonded geometry. -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.
Re: [gmx-users] impropers in Gromacs and acepype tool
On 3/6/14, 5:40 PM, Chetan Mahajan wrote: Thanks, Justin. I do not have AMBER parameter set or .rtp file. I have just one .top file which contains topologies and parameters. Just curious: where to get Amber parameter set from? If you have Gromacs, you have these parameters. Look in the /share/gromacs/top subdirectory of your Gromacs installation. The manual describes the contents of all the files. -Justin On Thu, Mar 6, 2014 at 4:25 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/6/14, 5:16 PM, Chetan Mahajan wrote: Hi I just wanted to check the order of atoms in a improper in gromacs input file *.top. According to urea example on page 137 ( section 5.7)of manual 4.6.4, order of i,j,k,l atoms in improper always starts with central atom, whereas that in a *.top file generated with acepype lists i,j,k,l order for improper in formate ion as H O C O. Central atom at third position. Is this right or bug in the tool acepype? It's right. The example in the manual is for Gromos force fields. You should look at the actual .rtp files for the AMBER parameter set you're trying to use. Suffice it to say that different atom orders are supported, because the Gromacs machinery (specifically pdb2gmx) knows how to deal with lots of stuff based on bonded geometry. -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. -- == 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.
Re: [gmx-users] impropers in Gromacs and acepype tool
On 3/6/14, 5:42 PM, Chetan Mahajan wrote: I think acepype Amber2gromacs tool has amber parameter files. but here is no .rtp What I am referring to are standard Gromacs force field files that come with the Gromacs software. If you intend to use Gromacs for your simulations, you would do well to read the manual about what these files are and how they are used. Understanding their contents would have cleared up several of your questions already. -Justin On Thu, Mar 6, 2014 at 4:40 PM, Chetan Mahajan chetanv...@gmail.com wrote: Thanks, Justin. I do not have AMBER parameter set or .rtp file. I have just one .top file which contains topologies and parameters. Just curious: where to get Amber parameter set from? On Thu, Mar 6, 2014 at 4:25 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/6/14, 5:16 PM, Chetan Mahajan wrote: Hi I just wanted to check the order of atoms in a improper in gromacs input file *.top. According to urea example on page 137 ( section 5.7)of manual 4.6.4, order of i,j,k,l atoms in improper always starts with central atom, whereas that in a *.top file generated with acepype lists i,j,k,l order for improper in formate ion as H O C O. Central atom at third position. Is this right or bug in the tool acepype? It's right. The example in the manual is for Gromos force fields. You should look at the actual .rtp files for the AMBER parameter set you're trying to use. Suffice it to say that different atom orders are supported, because the Gromacs machinery (specifically pdb2gmx) knows how to deal with lots of stuff based on bonded geometry. -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. -- == 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.
[gmx-users] angle between benzene rings
Dear gromacs users I would like to compute the angle of orientation between two benzene rings that I have simulated using gromacs. I think, for this, I have to get the vector normal to the plane of the benzene ring and then get the angle of among the unit vectors. Is there any tools in gromacs that can help me to do this? Does g_sgangle work here? Sanku -- 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] angle between benzene rings
On 3/6/14, 6:14 PM, Sanku M wrote: Dear gromacs users I would like to compute the angle of orientation between two benzene rings that I have simulated using gromacs. I think, for this, I have to get the vector normal to the plane of the benzene ring and then get the angle of among the unit vectors. Is there any tools in gromacs that can help me to do this? Does g_sgangle work here? That's what g_sgangle -oa claims to do. Have you tried it? -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.
Re: [gmx-users] Generate many random configurations
You are right...it is physically unreasonable for the particles to occupy the same space. I will not be running any MD simulations with the configurations that I am generating. I will only use the configurations to determine the coordination number -- the goal is to emulate an ideal gas, but with a nonspherical solute shape. The initial configuration contains the coordinates of the carbon atoms of a single tert-butanol (TBA) molecule. I would like to add x additional TBA molecules at random positions, including random orientations. Maybe the way I am doing this will not be feasible, because I really need particles to overlap such that the g(r) = 1 at all distances. I was trying to generate these random configurations in a clever way using GROMACS commands, instead of reinventing the wheel and writing my own program. Do you know of any available programs that may be of some assistance? Otherwise, I may end up writing my own. Thanks, Blake -- View this message in context: http://gromacs.5086.x6.nabble.com/Generate-many-random-configurations-tp5014976p5015010.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Generate many random configurations
On 3/6/14, 7:27 PM, rankinb wrote: You are right...it is physically unreasonable for the particles to occupy the same space. I will not be running any MD simulations with the configurations that I am generating. I will only use the configurations to determine the coordination number -- the goal is to emulate an ideal gas, but with a nonspherical solute shape. The initial configuration contains the coordinates of the carbon atoms of a single tert-butanol (TBA) molecule. I would like to add x additional TBA molecules at random positions, including random orientations. Maybe the way I am doing this will not be feasible, because I really need particles to overlap such that the g(r) = 1 at all distances. I was trying to generate these random configurations in a clever way using GROMACS commands, instead of reinventing the wheel and writing my own program. Do you know of any available programs that may be of some assistance? Otherwise, I may end up writing my own. So you basically need infinite sampling via some finite number of configurations. I doubt you'll get that with genbox. If you require g(r) = 1 for all positions, that's just a regular grid with atoms occupying every point at which the RDF is measured (every 0.002 nm in g_rdf, by default). I suppose one could try to generate enough random configurations that are different but do not enrich any particular site, but that sounds like a losing battle to me. So, in short, no, I can't think of a particularly clever or Gromacs-centric way to do this. Maybe someone else can, but it looks like you're trying to make genbox do something it's not likely to accomplish. -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.
[gmx-users] Regarding the change in number of processors of simulation job
Hello everyone, When I am restarting a simulation job after crash or extending simulation, if I increase number of processor then sharp change in coulomb potential (short range) is observed. But, if I keep the number of processor fixed then such thing is not found. My question is why this is observed? Secondly, do I have to always keep the number of processor fixed throughout the whole simulation? -- 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] MM-GB/SA analysis in Gromacs
Dear Andrea Spitaleri, I run protein-ligand complex for 20ns simulation in gromacs, i need to calculate the binding free energy calculation. I had a look at http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0046902 , and i want to calculate MM/PBSA binding free energy using the tool you mentioned... So I kindly request you sir, to provide the valuable help sir... My email id is: kannan.2...@gmail.com I am waiting for your reply. Many thanks in advance kannan s -- View this message in context: http://gromacs.5086.x6.nabble.com/MM-GB-SA-analysis-in-Gromacs-tp5003337p5015014.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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.
