Re: [gmx-users] Fwd: Regarding trjorder
I don't know what you are seeking, a definition of the first shell, or of how to analyse. Mark On Mar 3, 2014 6:08 AM, Venkat Reddy venkat...@gmail.com wrote: Hello, I have used the trjorder command to order water around 5 Angstrom radius of a protein. Can anyone suggest how the obtained pdb file can be used to analyse the system considering only this first shell of water around the protein? Please help me in this regard. Thanks -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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] Regarding structure analysis of DNA
Hai I have done simulation of DNA on carbon nano tube surface. I want to calculate structural changes (means changes in stacking, puckering angles and bending of helix) in DNA. Can any suggest me how to calculate these things. Thank You Very Much. regards M.SathishKumar -- 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] gromacs.org_gmx-users Digest, Vol 119, Issue 8
gromacs.org_gmx-users-requ...@maillist.sys.kth.se wrote:
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Today's Topics:
1. Regarding structure analysis of DNA (Sathish Kumar)
2. Set the environment variables of FFTW3_INCLUDE_DIR and
FFTW3_LIBRARIES (Hassan Aaryapour)
--
Message: 1
Date: Mon, 3 Mar 2014 01:05:41 -0800
From: Sathish Kumar sathishk...@gmail.com
To: Discussion list for GROMACS users gmx-us...@gromacs.org
Subject: [gmx-users] Regarding structure analysis of DNA
Message-ID:
CAFi=hwk79kpmzoy9nceko+qf+9xummuztwoya8pmragbnhb...@mail.gmail.com
Content-Type: text/plain; charset=ISO-8859-1
Hai
I have done simulation of DNA on carbon nano tube surface. I want
to calculate structural changes (means changes in stacking, puckering
angles and bending of helix) in DNA. Can any suggest me how to calculate
these things.
Thank You Very Much.
regards
M.SathishKumar
--
Message: 2
Date: Mon, 3 Mar 2014 13:56:01 +0330
From: Hassan Aaryapour hassan.grom...@gmail.com
To: gromacs.org_gmx-users
gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Set the environment variables of
FFTW3_INCLUDE_DIR and FFTW3_LIBRARIES
Message-ID:
cacqaq9-nsm-extkcpwyr6khr1+0t75x4nw0mbrunlxhc_eh...@mail.gmail.com
Content-Type: text/plain; charset=ISO-8859-1
Dear Gmx-user;
I want to install double precision gromacs 4.5.3 and FFTW 3.3.2 in my
home directory.
first, according to the FFTW installation instructions I installed and
introduced it to bash shell it as the following order:
$tar -xzvf fftw-3.3.2.tar.gz
$./configure --enable-threads --prefix=/home/WeNMR/ProgramFiles/fftw
$make
$make install
export CPPFLAGS=-I/home/WeNMR/ProgramFiles/fftw/include
export LDFLAGS=-L/home/WeNMR/ProgramFiles/fftw/lib
but it isn't found automatically by cmake when I want to install gromacs.
and this error was appeared:
CMake Error at
/usr/local/share/cmake-2.8/Modules/FindPackageHandleStandardArgs.cmake:108
(message):
Could not find FFTW3. Provide the fftw3 install directory in the
FFTW3_ROOT_DIR environment variable. (missing: FFTW3_LIBRARIES
FFTW3_INCLUDE_DIR)
Call Stack (most recent call first):
/usr/local/share/cmake-2.8/Modules/FindPackageHandleStandardArgs.cmake:315
(_FPHSA_FAILURE_MESSAGE)
cmake/FindFFTW3.cmake:31 (find_package_handle_standard_args)
CMakeLists.txt:636 (find_package)
How can I set the environment variables for FFTW3_INCLUDE_DIR and
FFTW3_LIBRARIES?
can I add my FFTW installed path to CMakeLists.txt file in the
related section in below? how?
if(${GMX_FFT_LIBRARY} STREQUAL FFTW3)
#MESSAGE(STATUS Using external FFT library - fftw3)
if(GMX_DOUBLE)
find_package(FFTW3 REQUIRED)
include_directories(${FFTW3_INCLUDE_DIR})
set(FFT_LIBRARIES ${FFTW3_LIBRARIES})
set(PKG_FFT fftw3)
else(GMX_DOUBLE)
find_package(FFTW3F REQUIRED)
include_directories(${FFTW3F_INCLUDE_DIR})
set(FFT_LIBRARIES ${FFTW3F_LIBRARIES})
set(PKG_FFT fftw3f)
endif(GMX_DOUBLE)
Thank you in advance
Hassan
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Re: [gmx-users] .top file after using amber2gromacs
On 3/3/14, 12:33 AM, Chetan Mahajan wrote: Thank you, Justin. Could you also tell me if atomtypes section is needed at all? (sample .top file on gromacs website does not have it). If you have additional atom types that are not part of the parent force field, yes, it is necessary. -Justin regards Chetan On Sun, Mar 2, 2014 at 10:32 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/2/14, 11:24 PM, Chetan Mahajan wrote: Hi All I have gromacs files generated using acpype tool acting on Amber files originally. I need to know the meaning of certain terms in that *.top file (email with attachment of .top file got blocked due to attachment). Unfortunately, I can't find on the web, any material regarding that. It would be great, if anyone could comment on the following. *1. What is the meaning of terms under defaults option at the top of the file (pasted below)?* [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 12 yes 0.5 0.8333 Please refer to manual section 5.7.1, where each of these terms is explained after the urea.top example. * 2a. ** Is atomtypes section needed? (sample .top file on gromacs website does not have it) (pasted after 2b question)**In this atomtypes section, the Amber2gromacs tool keeps mass and charge of each atom as zero. Would a simulation with these places zero be a valid simulation **?* My guess is yes. THis is since, corresponding values are available later in atoms section. The purpose of asking this question is that I have to be sure of the runs I have made, that nothing has gone wrong in having those zeros. Charge and mass information in [atomtypes] is indeed over-written by whatever is found in [atoms]. You can always confirm what has been used by obtaining the grompp-processed topology with grompp -pp or by using gmxdump on the .tpr file. * 2b.I see several enigmatic terms such as bond type p type, Amb. Can you explain these terms, if they are necessary at all? Why last two columns for Amb?* Different force fields work in different ways, so the Gromacs file format is standard across all the different force fields. Since there are generally fewer types of bonded interactions, bonded types are a subset of nonbonded types. Sometimes there are no differences, as is the case here. If a force field uses separate bonded and nonbonded types, that just means the bonded types are an interpretation of the atom types used within ffbonded.itp. The ptype column is particle type - A for atoms, S for shells, V for virtual sites. The last two columns are a comment, likely the original AMBER parameters so you can verify the unit conversion. (part of the data for both 2a and 2b pasted below) [ atomtypes ] ;name bond_type mass charge ptype sigma epsilon Amb Ti Ti 0.0 0.0 A 1.39461e-01 6.08772e-02 ; 0.78 0.0145 OT OT 0.0 0.0 A 2.87832e-01 8.29687e-02 ; 1.62 0.0198 HW HW 0.0 0.0 A 0.0e+00 0.0e+00 ; 0.00 0. *4.WHat is cgnr? how is it different from nr? (it appears in atoms section, example below)* cgnr = charge group number nr = atom number -Justin nr type resi res atom cgnr charge mass ; qtot bond_type 1 Ti 1 iO2TI1 1.691002 47.86700 ; qtot 1.691 Thanks -- == 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
Re: [gmx-users] Regarding structure analysis of DNA
On 3/3/14, 4:05 AM, Sathish Kumar wrote: Hai I have done simulation of DNA on carbon nano tube surface. I want to calculate structural changes (means changes in stacking, puckering angles and bending of helix) in DNA. Can any suggest me how to calculate these things. Chapter 8 describes all available analysis tools. For more complicated things, you may need outside software like MDAnalysis or similar packages. -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] Problems with periodic syatems
Hi all, I am having trouble to simulate the periodic system with the gmxV-4.6.3. I am running the simulation in GPU's. Every time there has a problem with the bonded interaction like that given below- ### Program mdrun_omp, VERSION 4.6.3 Source code file: /usr/local/programs/gromacs/gromacs-4.6.3/src/gromacs-4.6.3/src/mdlib/domdec_top.c, line: 393 Fatal error: 1 of the 103102 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off dist ance (0.528 nm) or the two-body cut-off distance (1.056 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors # But when I was running without a periodic system, it was okay. Could somebody please help me to get rid of this. The problem might come due the domain decomposition problem. I saw somewhere that the domain decomposition algorithm doesn't work properly for the periodic systems. thanks in advance. -- Susanta Haldar Institute of Organic Chemistry and Biochemistry Academy of Sciences of the Czech Republic. -- 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] Apple cluster
I have four quadcore apple computers and I have been informed that Apple has a Qmaster software ( in their Final Cut Studio package) that can do distributed processing. Has anyone attempted this with Apple using Gromacs??? Is this feasible?? I have only worked with Linux systems (and have used MPICH, MPI)..I am not an expert, but would really appreciate some comments/advice from someone who knows the basics here.. Is the fact that Apple has just started this mean there are a lot of bugs in the system? Cost-wise and energy-wise do you think it would be smarter to invest in a small Linux cluster (~ 20-30 nodes) than to assemble this Apple cluster? Thanks, Steve -- View this message in context: http://gromacs.5086.x6.nabble.com/Apple-cluster-tp5014900.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] Error Mdrun
On 3/3/14, 12:39 PM, Andres Ortega wrote: Dear Gromacs Users, I was trying to run a simulation , but this NOTE came out: 1 GPU detected: #0: NVIDIA GeForce GT 330, compute cap.: 1.2, ECC: no, stat: incompatible (This mean i cant use this GPU, or GROMACS it is not install well?) It means the GPU is not compatible, so you can't use it. There is no indication of any problem with the installation. The minimum compute capacity required is 2.0. -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] md_pull code in umbrella sampling
It's not US if you have a non-zero pull-rate1 that gets applied during your simulation, although with your pull-geometry=distance I don't think that pull-rate is even used (therefore I think that part is technically correct, although your .mdp file is confusing on this issue). Careful that X and Y are going to be free to diffuse introducing what will likely be a convergence nightmare for separation distances at which the drug and protein are just coming into contact. Specifically, while you may set up the system with the drug and protein having the same COM in X and Y, that will change over time (more or less, depending on what define = -DPOSRES_Protein does for your system). This likely isn't a problem for large separation distances (although there will be some convergence issues here due to the need to sample over all X/Y at some larger displacements for which coulomb interaction are still non-negligable). Neither is it likely to be a problem for umbrellas in which the protein constrains your drug within a favourable binding pocket. However, in umbrellas where the drug and protein just come into contact, you will probably start with contact, but then need to obtain the proper boltzmann populations for interactions that depend on X/Y. What's worse , if you end up predominantly sampling conformational space that overlaps along your order parameter (Z) but not in some other orthogonal degree of freedom (e.g., X/Y), then your PMF will be simply wrong (that will get fixed with extensive sampling, but the amount of sampling that you need might be unobtainably large). Personally, I would solve this by adding a second pull group with a flat-bottom potential that acts only on X and Y to keep the drug within a cylinder that extends along Z away from your protein. However, you would need to modify gromacs source code for this (I have some posts on the uses lists over the years about how to do this). An alternative solution is to define an order parameter that acts in all 3 dimensions, although you may need to compute the free energy of releasing this restraint (a) in the binding pocket and (b) at large separations where your PMF flattens out to zero. Careful also about gen_vel = no (i.e., be sure to load in velocities if you are not generating them) Chris. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Arunima Shilpi writetoas...@gmail.com Sent: 03 March 2014 09:34 To: gmx-us...@gromacs.org Subject: [gmx-users] md_pull code in umbrella sampling Dear Sir I am trying to calculate the potential mean force (PMF) between protein and Ligand. I have applied position restrain to protein. I have applied reference pulling group to Protein and Pulling force has been applied to ligand. The pul force is applied along Z-axis. I had query as to whether I am proceeding in the right direction. Here I have provided the detail of the content of md_pull.mdp md_pull.mdp title = Umbrella pulling simulation define = -DPOSRES_Protein ; Run parameters integrator = md dt = 0.002 tinit = 0 nsteps = 25; 500 ps nstcomm = 10 ; Output parameters nstxout = 5000 ; every 10 ps nstvout = 5000 nstfout = 500 nstxtcout = 500 ; every 1 ps nstenergy = 500 ; Bond parameters constraint_algorithm= lincs constraints = all-bonds continuation= yes ; continuing from NPT ; Single-range cutoff scheme nstlist = 5 ns_type = grid rlist = 1.4 rcoulomb= 1.4 rvdw= 1.4 ; PME electrostatics parameters coulombtype = PME fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on in two groups Tcoupl = Nose-Hoover tc_grps = Protein Non-Protein tau_t = 0.5 0.5 ref_t = 310 310 ; Pressure coupling is on Pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 refcoord_scaling = com ; Generate velocities is off gen_vel = no ; Periodic boundary conditions are on in all directions pbc = xyz ; Long-range dispersion correction DispCorr= EnerPres ; 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 = Protein pull_group1 = DRG pull_rate1 = 0.01 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 1000 ; kJ mol^-1 nm^-2 Regards Arunima -- 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
Re: [gmx-users] No default U-B types charmm
On Mon, Mar 3, 2014 at 7:25 PM, gromacs query gromacsqu...@gmail.comwrote: Hi Justin Its problem with the waters I think. Can't be, they have no U-B. I found conflict in water atom names: charmm36-jan2014.ff/tip3p.itp: 1 OT 1 SOL OW 1 -0.834 2 HT 1 SOL HW1 10.417 3 HT 1 SOL HW2 10.417 charmm36-jan2014.ff/merged.itp [ TIP3 ] [ atoms ] OH2OT -0.834 0 H1HT0.417 1 H2HT0.417 2 In PDB from charmgui its OH2,H1,H2. I changed names in charmm36-jan2014.ff/tip3p.itp as in merged.rtp but still I get same error. On Mon, Mar 3, 2014 at 5:46 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/3/14, 10:57 AM, gromacs query wrote: Hi All I am trying to use charmm36 (charmm36-jan2014 from charmm website) with popc membrane built using charmm-gui (have water and ions). I used commands as follows: pdb2gmx -f step5_assembly.pdb -o popc.gro -water tip3p -ff charmm36-jan2014 editconf -f popc.gro -o popc_box.gro -c -d 0.0 grompp -f minim.mdp -c popc_box.gro -p topol.top -o em.tpr I get this error: (so many) ERROR 11520 [file topol.top, line 184419]: No default U-B types What atom numbers are on line 184419? What atom types are they in the [atoms] section for that [moleculetype]? Mark Where are UB for charmm36? This shouldn't happen. Can you please identify what atoms are causing the failure? It may help to simplify by working only with a single lipid rather than a full membrane. -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.
Re: [gmx-users] Two-body Bonded Distance
Where are you adding the virtual particle in relation to all of this? The virtual particle is included in the ligand residue (#160) but this error occurs in whichever methionine residue has the longest CB-CE distance. They are not spatially near one another and the offending residue is different from trajectory to trajectory given the fluctuations of the MET side chains. -- View this message in context: http://gromacs.5086.x6.nabble.com/Two-body-Bonded-Distance-tp5014864p5014907.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] Problems with periodic syatems
Much more likely your initial conditions are unsuited for applying periodicity, such as overlapping atoms e.g. from insufficient extra space around the atoms at the edges of the box. And next time, please link to I saw somewhere that... (coz that was probably wrong or out of context). Mark On Mon, Mar 3, 2014 at 5:14 PM, susanta haldar susantahal...@gmail.comwrote: Hi all, I am having trouble to simulate the periodic system with the gmxV-4.6.3. I am running the simulation in GPU's. Every time there has a problem with the bonded interaction like that given below- ### Program mdrun_omp, VERSION 4.6.3 Source code file: /usr/local/programs/gromacs/gromacs-4.6.3/src/gromacs-4.6.3/src/mdlib/domdec_top.c, line: 393 Fatal error: 1 of the 103102 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off dist ance (0.528 nm) or the two-body cut-off distance (1.056 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors # But when I was running without a periodic system, it was okay. Could somebody please help me to get rid of this. The problem might come due the domain decomposition problem. I saw somewhere that the domain decomposition algorithm doesn't work properly for the periodic systems. thanks in advance. -- Susanta Haldar Institute of Organic Chemistry and Biochemistry Academy of Sciences of the Czech Republic. -- 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] antiparallel beta sheet
Dear users, I would like to analyse the time variation of antiparallel beta sheet formation. I am aware that dssp and stride program can calculate the beta sheet content but is there a tool that can distinguish between antiparallel and parallel beta sheet (in terms of giving numeric value as output and not through visual inspection)? Thanks in advance. Nidhi -- 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] Option:Coupled to heme
On 3/3/14, 2:23 PM, Gmail2 wrote: That is, option 3 is not deprotonated. Am I wrong? Not fully deprotonated to the point of being anionic, no. Look at the .rtp entry - it is identical to HISA. Then, how can I get deprotonated histidine? Find a force field that has such a thing, or parametrize it yourself. -Justin Ahmet Yıldırım 3 Mar 2014 tarihinde 20:43 saatinde, Justin Lemkul jalem...@vt.edu şunları yazdı: On 3/3/14, 1:33 PM, Gmail2 wrote: Dear users, When I use the -his option of pdb2gmx for deprotonated the Histidine residue, I get the following options: 0. H on ND1 only (HISA) 1. H on NE2 only (HISB) 2. H on ND1 and NE2 (HISH) 3. Coupled to Heme (HIS1) Where option 3 is deprotonated. But it is named as a 'Coupled to heme'. Why option 3's name is not deprotonated HIS? Because it's not. HIS1 is just a delta-protonated histidine. The different name (HIS1 vs. HISA) is required for specbond.dat to work properly. -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] Two-body Bonded Distance
On 3/3/14, 1:52 PM, jolayfield wrote: Where are you adding the virtual particle in relation to all of this? The virtual particle is included in the ligand residue (#160) but this error occurs in whichever methionine residue has the longest CB-CE distance. They are not spatially near one another and the offending residue is different from trajectory to trajectory given the fluctuations of the MET side chains. There's no reason that I can think of that adjustments to one molecule should affect two-body interactions in a different molecule. Sounds buggy. Please file an bug report on redmine.gromacs.org with all the files necessary to reproduce it so it can be examined. -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] antiparallel beta sheet
On 3/3/14, 2:02 PM, Nidhi Katyal wrote: Dear users, I would like to analyse the time variation of antiparallel beta sheet formation. I am aware that dssp and stride program can calculate the beta sheet content but is there a tool that can distinguish between antiparallel and parallel beta sheet (in terms of giving numeric value as output and not through visual inspection)? You can define an order parameter between 0 and 1 to discriminate between the two. It is fairly common in simulation literature of amyloids. -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] No default U-B types charmm
What atom numbers are on line 184419? What atom types are they in the [atoms] section for that [moleculetype]? These are waters only (I am using tipS3p CHARMM TIP3P). UB should not be there. I am following Justin's suggestion to remove moleculetype from top file (still not solved and trying, will let you know; I am newbie to gromacs) thanks On Mon, Mar 3, 2014 at 6:48 PM, Mark Abraham mark.j.abra...@gmail.comwrote: On Mon, Mar 3, 2014 at 7:25 PM, gromacs query gromacsqu...@gmail.com wrote: Hi Justin Its problem with the waters I think. Can't be, they have no U-B. I found conflict in water atom names: charmm36-jan2014.ff/tip3p.itp: 1 OT 1 SOL OW 1 -0.834 2 HT 1 SOL HW1 10.417 3 HT 1 SOL HW2 10.417 charmm36-jan2014.ff/merged.itp [ TIP3 ] [ atoms ] OH2OT -0.834 0 H1HT0.417 1 H2HT0.417 2 In PDB from charmgui its OH2,H1,H2. I changed names in charmm36-jan2014.ff/tip3p.itp as in merged.rtp but still I get same error. On Mon, Mar 3, 2014 at 5:46 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/3/14, 10:57 AM, gromacs query wrote: Hi All I am trying to use charmm36 (charmm36-jan2014 from charmm website) with popc membrane built using charmm-gui (have water and ions). I used commands as follows: pdb2gmx -f step5_assembly.pdb -o popc.gro -water tip3p -ff charmm36-jan2014 editconf -f popc.gro -o popc_box.gro -c -d 0.0 grompp -f minim.mdp -c popc_box.gro -p topol.top -o em.tpr I get this error: (so many) ERROR 11520 [file topol.top, line 184419]: No default U-B types What atom numbers are on line 184419? What atom types are they in the [atoms] section for that [moleculetype]? Mark Where are UB for charmm36? This shouldn't happen. Can you please identify what atoms are causing the failure? It may help to simplify by working only with a single lipid rather than a full membrane. -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.
[gmx-users] tip5p and charmm
Hi all, I saw a post from a little while ago where someone (Justin?) said that tip5p wasnt recommended for use with charmm27, so tip5p wanst included in the watermodels.dat file. I have found that my system blows up with tip5p, but tip4p and tip3p energy minimize just fine. And, I am also having problems getting pymol and chimera to open the .gro file produced by mdrun with tip4p and tip5p. (VMD opens the .gro file fine.) My questions are, is tip5p/charmm27 a good combination to use when trying to model protein-prosthetic.group-water interactions? And, is VMD my only option for visualizing the 4 and 5 point water models? Thanks! -- 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] dna with charmm36
Hi All Its in continuation. I am confused about something. In PDB file obtained from NAB in AMBER I removed all Hydrogens and allow pdb2gmx to add them. PDB has DC5 as starting and DT3 as end residue and I get this error: pdb2gmx -ter -ff charmm36-jan2014 -f test.pdb -o test.gro ( with or without -ignh) WARNING: atom H3' is missing in residue DC5 1 in the pdb file You might need to add atom H3' to the hydrogen database of building block DC5 in the file merged.hdb (see the manual) WARNING: atom H5'1 is missing in residue DT3 10 in the pdb file You might need to add atom H5'1 to the hydrogen database of building block DT3 in the file merged.hdb (see the manual) I found DC5 and others (D*5 and D*3) are missing in merged.hdb. Are these missing or intentionally not added? Also if I change name of DC5 to DC and DT3 to DT it works fine and all Hs are added without error. thanks JIom On Wed, Feb 5, 2014 at 3:53 PM, gromacs query gromacsqu...@gmail.comwrote: need a coffee! On Wed, Feb 5, 2014 at 3:44 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/5/14, 10:42 AM, gromacs query wrote: Hi Justin I forgot to ask about waters. With charmm36 it give these options: 1: TIP3P TIP 3-point, recommended, by default uses CHARMM TIP3 with LJ on H 2: TIP4P TIP 4-point 3: TIP5P TIP 5-point 4: SPC simple point charge 5: SPC/E extended simple point charge 6: None I want to use TIPs3P water (so called Charmm TIP3P). So if I select option 1:TIP3P it will be simple TIP3P without LJs on H (please correct me). How to force default option which is CHARMM TIP3 with LJs on Hs? Incorrect - read the description again. CHARMM TIP3P is default when using CHARMM. -Justin -- == Justin A. Lemkul, Ph.D. 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] dna with charmm36
On 3/3/14, 7:57 PM, gromacs query wrote: Hi All Its in continuation. I am confused about something. In PDB file obtained from NAB in AMBER I removed all Hydrogens and allow pdb2gmx to add them. PDB has DC5 as starting and DT3 as end residue and I get this error: pdb2gmx -ter -ff charmm36-jan2014 -f test.pdb -o test.gro ( with or without -ignh) WARNING: atom H3' is missing in residue DC5 1 in the pdb file You might need to add atom H3' to the hydrogen database of building block DC5 in the file merged.hdb (see the manual) WARNING: atom H5'1 is missing in residue DT3 10 in the pdb file You might need to add atom H5'1 to the hydrogen database of building block DT3 in the file merged.hdb (see the manual) I found DC5 and others (D*5 and D*3) are missing in merged.hdb. Are these missing or intentionally not added? Also if I change name of DC5 to DC and DT3 to DT it works fine and all Hs are added without error. Specific naming of terminal residues like this is not needed for CHARMM. Just choose the correct termini (5TER and 3TER) and they will be patched appropriately. -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] tip5p and charmm
On 3/3/14, 7:07 PM, Rafael I. Silverman y de la Vega wrote: Hi all, I saw a post from a little while ago where someone (Justin?) said that tip5p wasnt recommended for use with charmm27, so tip5p wanst included in the watermodels.dat file. I have found that my system blows up with tip5p, but tip4p and tip3p energy minimize just fine. And, I am also having problems getting pymol and chimera to open the .gro file produced by mdrun with tip4p and tip5p. (VMD opens the .gro file fine.) My questions are, is tip5p/charmm27 a good combination to use when trying to model protein-prosthetic.group-water interactions? Doubtful. Clearly your findings indicate the combination is not stable, and that is my recollection from previous posts on the list, as well. We develop CHARMM in the context of TIP3P. If something else happens fortuitously to work, great, but that's coincidence. People have used other water models and have reported some levels of success (stable simulations, at least), but it's not what we recommend because it's not consistent with the parametrization. -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] dna with charmm36
Hi Justin Yes I chose termini 5TER or 3TER correctly but it only works fine when D*5 replaced by D* and D*3 by D* otherwise it ends with errors as said previously. thanks JIom On Tue, Mar 4, 2014 at 1:00 AM, Justin Lemkul jalem...@vt.edu wrote: On 3/3/14, 7:57 PM, gromacs query wrote: Hi All Its in continuation. I am confused about something. In PDB file obtained from NAB in AMBER I removed all Hydrogens and allow pdb2gmx to add them. PDB has DC5 as starting and DT3 as end residue and I get this error: pdb2gmx -ter -ff charmm36-jan2014 -f test.pdb -o test.gro ( with or without -ignh) WARNING: atom H3' is missing in residue DC5 1 in the pdb file You might need to add atom H3' to the hydrogen database of building block DC5 in the file merged.hdb (see the manual) WARNING: atom H5'1 is missing in residue DT3 10 in the pdb file You might need to add atom H5'1 to the hydrogen database of building block DT3 in the file merged.hdb (see the manual) I found DC5 and others (D*5 and D*3) are missing in merged.hdb. Are these missing or intentionally not added? Also if I change name of DC5 to DC and DT3 to DT it works fine and all Hs are added without error. Specific naming of terminal residues like this is not needed for CHARMM. Just choose the correct termini (5TER and 3TER) and they will be patched appropriately. -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] dna with charmm36
On 3/3/14, 8:13 PM, gromacs query wrote: Hi Justin Yes I chose termini 5TER or 3TER correctly but it only works fine when D*5 replaced by D* and D*3 by D* otherwise it ends with errors as said previously. As I would expect. Specific D*5/D*3 names are for AMBER force fields only. -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] gromacs.org_gmx-users Digest, Vol 119, Issue 10
Thanks Justin!
The result about the improper dihedral angle from ParamChem does keep
me very confused. For the molecule (C6H5-NH2), the one of N H H C should
not have improper dihedral however the websever showes there is one.
If anyone has the experience of Charmm improper dihedral, please give a
help. Thanks!
Thom
On Mon, Mar 3, 2014 at 9:57 AM,
gromacs.org_gmx-users-requ...@maillist.sys.kth.se wrote:
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than Re: Contents of gromacs.org_gmx-users digest...
Today's Topics:
1. Re: Regarding structure analysis of DNA (Justin Lemkul)
2. Re: Set the environment variables of FFTW3_INCLUDE_DIR and
FFTW3_LIBRARIES (Justin Lemkul)
3. Re: Two-body Bonded Distance (jolayfield)
4. Re: Question about Improper Dihedral of Charmm in gmx
ParamChem (Justin Lemkul)
5. md_pull code in umbrella sampling (Arunima Shilpi)
6. No default U-B types charmm (gromacs query)
--
Message: 1
Date: Mon, 03 Mar 2014 09:14:51 -0500
From: Justin Lemkul jalem...@vt.edu
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Regarding structure analysis of DNA
Message-ID: 53148e5b.8010...@vt.edu
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 3/3/14, 4:05 AM, Sathish Kumar wrote:
Hai
I have done simulation of DNA on carbon nano tube surface. I
want
to calculate structural changes (means changes in stacking, puckering
angles and bending of helix) in DNA. Can any suggest me how to calculate
these things.
Chapter 8 describes all available analysis tools. For more complicated
things,
you may need outside software like MDAnalysis or similar packages.
-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
==
--
Message: 2
Date: Mon, 03 Mar 2014 09:16:53 -0500
From: Justin Lemkul jalem...@vt.edu
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Set the environment variables of
FFTW3_INCLUDE_DIR and FFTW3_LIBRARIES
Message-ID: 53148ed5.2050...@vt.edu
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 3/3/14, 5:26 AM, Hassan Aaryapour wrote:
Dear Gmx-user;
I want to install double precision gromacs 4.5.3 and FFTW 3.3.2 in my
home directory.
first, according to the FFTW installation instructions I installed and
introduced it to bash shell it as the following order:
$tar -xzvf fftw-3.3.2.tar.gz
$./configure --enable-threads --prefix=/home/WeNMR/ProgramFiles/fftw
$make
$make install
export CPPFLAGS=-I/home/WeNMR/ProgramFiles/fftw/include
export LDFLAGS=-L/home/WeNMR/ProgramFiles/fftw/lib
but it isn't found automatically by cmake when I want to install gromacs.
and this error was appeared:
CMake Error at
/usr/local/share/cmake-2.8/Modules/FindPackageHandleStandardArgs.cmake:108
(message):
Could not find FFTW3. Provide the fftw3 install directory in the
FFTW3_ROOT_DIR environment variable. (missing: FFTW3_LIBRARIES
FFTW3_INCLUDE_DIR)
Call Stack (most recent call first):
/usr/local/share/cmake-2.8/Modules/FindPackageHandleStandardArgs.cmake:315
(_FPHSA_FAILURE_MESSAGE)
cmake/FindFFTW3.cmake:31 (find_package_handle_standard_args)
CMakeLists.txt:636 (find_package)
How can I set the environment variables for FFTW3_INCLUDE_DIR and
FFTW3_LIBRARIES?
Those are CMake command-line options. See the full installation
instructions
online, specifically
http://www.gromacs.org/Documentation/Installation_Instructions#4.4._Helping_CMake_find_the_right_libraries.2fheaders.2fprograms
Is there any reason you are installing outdated versions of Gromacs and
FFTW?
-Justin
can I add my FFTW installed path to CMakeLists.txt file in the
related section in below? how?
if(${GMX_FFT_LIBRARY} STREQUAL FFTW3)
#MESSAGE(STATUS Using external FFT library - fftw3)
if(GMX_DOUBLE)
find_package(FFTW3 REQUIRED)
include_directories(${FFTW3_INCLUDE_DIR})
set(FFT_LIBRARIES
Re: [gmx-users] REMD Melting Curve
On 2014-03-04 00:20, atanu_das wrote: Dear Gromacs users, I have performed a REMD simulation with 12 replicas exponentially spaced between 260-420K. However, when I applied g_kinetics program to generate the melting curve, I got 161 values starting from 260K to 420K having the folded fraction reported at each temperature. My question is if I am applying 12 replicas exponentially spaced in the temperature range chosen, how could I get 161 values? Am I doing something wrong? Does g_kinetics in GROMACS use any smoothing function to generate the intermediate temperature and folded fraction values? Please suggest/advise. Atanu What kind of values? You get one fraction folded per replica, right? Did you succesfully run the demux.pl? -- View this message in context: http://gromacs.5086.x6.nabble.com/REMD-Melting-Curve-tp5014920.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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] Set the environment variables of FFTW3_INCLUDE_DIR and FFTW3_LIBRARIES
Dear Justin
Thank you for your assistance, I run most of my MD simulations on the
WeNMR server, which have double precision gromacs ver 4.5.3.
Thanks again
hassan
On 3/3/14, Justin Lemkul jalem...@vt.edu wrote:
On 3/3/14, 5:26 AM, Hassan Aaryapour wrote:
Dear Gmx-user;
I want to install double precision gromacs 4.5.3 and FFTW 3.3.2 in my
home directory.
first, according to the FFTW installation instructions I installed and
introduced it to bash shell it as the following order:
$tar -xzvf fftw-3.3.2.tar.gz
$./configure --enable-threads --prefix=/home/WeNMR/ProgramFiles/fftw
$make
$make install
export CPPFLAGS=-I/home/WeNMR/ProgramFiles/fftw/include
export LDFLAGS=-L/home/WeNMR/ProgramFiles/fftw/lib
but it isn't found automatically by cmake when I want to install gromacs.
and this error was appeared:
CMake Error at
/usr/local/share/cmake-2.8/Modules/FindPackageHandleStandardArgs.cmake:108
(message):
Could not find FFTW3. Provide the fftw3 install directory in the
FFTW3_ROOT_DIR environment variable. (missing: FFTW3_LIBRARIES
FFTW3_INCLUDE_DIR)
Call Stack (most recent call first):
/usr/local/share/cmake-2.8/Modules/FindPackageHandleStandardArgs.cmake:315
(_FPHSA_FAILURE_MESSAGE)
cmake/FindFFTW3.cmake:31 (find_package_handle_standard_args)
CMakeLists.txt:636 (find_package)
How can I set the environment variables for FFTW3_INCLUDE_DIR and
FFTW3_LIBRARIES?
Those are CMake command-line options. See the full installation
instructions
online, specifically
http://www.gromacs.org/Documentation/Installation_Instructions#4.4._Helping_CMake_find_the_right_libraries.2fheaders.2fprograms
Is there any reason you are installing outdated versions of Gromacs and
FFTW?
-Justin
can I add my FFTW installed path to CMakeLists.txt file in the
related section in below? how?
if(${GMX_FFT_LIBRARY} STREQUAL FFTW3)
#MESSAGE(STATUS Using external FFT library - fftw3)
if(GMX_DOUBLE)
find_package(FFTW3 REQUIRED)
include_directories(${FFTW3_INCLUDE_DIR})
set(FFT_LIBRARIES ${FFTW3_LIBRARIES})
set(PKG_FFT fftw3)
else(GMX_DOUBLE)
find_package(FFTW3F REQUIRED)
include_directories(${FFTW3F_INCLUDE_DIR})
set(FFT_LIBRARIES ${FFTW3F_LIBRARIES})
set(PKG_FFT fftw3f)
endif(GMX_DOUBLE)
Thank you in advance
Hassan
--
==
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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