[gmx-users] gmx4.5.4 installation help
Hello gmx-users, I am trying to install gmx-4.5.4 on a HPC Linux cluster x86_64. 1. I installed fftw 3.2.2 ./configure --prefix /soft/sudip/abc/execs/fftw/ --enable-single --enable-threads 2. Installing Gromacs : CPPFLAGS and LDFLAGS were written in bashrc file a) ./configure --prefix=/soft/sudip/abc/execs/gromacs/ execute successfully without any complain. b) make /usr/bin/ld: /soft/sudip/abc/execs/fftw/lib/libfftw3f.a(apiplan.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC /soft/sudip/abc/execs/fftw/lib/libfftw3f.a: could not read symbols: Bad value collect2: ld returned 1 exit status make[3]: *** [libmd.la] Error 1 make[3]: Leaving directory `/soft/sudip/abc/untar/gromacs-4.5.4/src/mdlib' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/soft/sudip/abc/untar/gromacs-4.5.4/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/soft/sudip/abc/untar/gromacs-4.5.4/src' make: *** [all-recursive] Error 1 shows problem. Couldnot understand the origin of problem. Kndly let me know if some information is missing. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] gmx4.5.4 installation help
On 2/06/2011 5:03 PM, Chandan Choudhury wrote: Hello gmx-users, I am trying to install gmx-4.5.4 on a HPC Linux cluster x86_64. 1. I installed fftw 3.2.2 ./configure --prefix /soft/sudip/abc/execs/fftw/ --enable-single --enable-threads 2. Installing Gromacs : CPPFLAGS and LDFLAGS were written in bashrc file a) ./configure --prefix=/soft/sudip/abc/execs/gromacs/ execute successfully without any complain. b) make /usr/bin/ld: /soft/sudip/abc/execs/fftw/lib/libfftw3f.a(apiplan.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC /soft/sudip/abc/execs/fftw/lib/libfftw3f.a: could not read symbols: Bad value collect2: ld returned 1 exit status make[3]: *** [libmd.la http://libmd.la] Error 1 make[3]: Leaving directory `/soft/sudip/abc/untar/gromacs-4.5.4/src/mdlib' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/soft/sudip/abc/untar/gromacs-4.5.4/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/soft/sudip/abc/untar/gromacs-4.5.4/src' make: *** [all-recursive] Error 1 shows problem. Couldnot understand the origin of problem. Kndly let me know if some information is missing. See http://www.gromacs.org/Downloads/Installation_Instructions, where this problem is discussed. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] gmx4.5.4 installation help
The error message already shows some hints. Try recompile FFTW with -fPIC. Jianguo From: Chandan Choudhury iitd...@gmail.com To: gmx-users gmx-users@gromacs.org Sent: Thursday, 2 June 2011 15:03:03 Subject: [gmx-users] gmx4.5.4 installation help Hello gmx-users, I am trying to install gmx-4.5.4 on a HPC Linux cluster x86_64. 1. I installed fftw 3.2.2 ./configure --prefix /soft/sudip/abc/execs/fftw/ --enable-single --enable-threads 2. Installing Gromacs : CPPFLAGS and LDFLAGS were written in bashrc file a) ./configure --prefix=/soft/sudip/abc/execs/gromacs/ execute successfully without any complain. b) make /usr/bin/ld: /soft/sudip/abc/execs/fftw/lib/libfftw3f.a(apiplan.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC /soft/sudip/abc/execs/fftw/lib/libfftw3f.a: could not read symbols: Bad value collect2: ld returned 1 exit status make[3]: *** [libmd.la] Error 1 make[3]: Leaving directory `/soft/sudip/abc/untar/gromacs-4.5.4/src/mdlib' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/soft/sudip/abc/untar/gromacs-4.5.4/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/soft/sudip/abc/untar/gromacs-4.5.4/src' make: *** [all-recursive] Error 1 shows problem. Couldnot understand the origin of problem. Kndly let me know if some information is missing. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_rdf query
Hi ALL, I am using in calculating the distribution of a solvent around the COM of a protein chain using g_rdf. When I plot the output file (attached) I get a curve which increases first (from 1 to a value of about 2.5) and then decreases to x-axis values ranging from 1 to 5. If I understand correctly then x-axis values represent the radius of calculation around the protein. right? It says r. Whats its unit? And what does the y-axis values stand for? Can someone please explain me the g_rdf plot attached here. Thanks a lot in advance. Regards, Anirban attachment: try_rdf.jpg-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] viscosity
On Wed, 2011-06-01 at 23:37 +0200, Thomas Koller wrote: Hello, I calculate the viscosity with g_energy using option -vis (Gromacs 4.0.7): g_energy -f file.trr -s file.tpr -vis visc.xvg Why do I get viscosity values only until the half of the simulation time? This results from the method an autocorrelation function is averaged. For an average that is unbiased you need the same number of samples for every time step. You achieve this by shifting the choice of the value for t=0 through the trajectory. The maximal length of the average you can achieve with this is exactly half the simulation time. /Flo Thomas -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Enthalpy of vaporization
Hello all, I am trying to find the enthalpy of vaporization for 7 types of alcohols to try to compare to experimental values. I have all of them simulated to equilibrium and I can use g_energy to view the Total Energy (both kinetic and potential). In order for me to find the enthalpy of vaporization, is it as simple as just running the NPT script again and changing the temperature to that of its boiling point and 1 degree K over that? Would it just be the difference between the enthalpy at boiling pt and 1 degree past boiling? If anyone could possibly lead me in the right direction I would greatly appreciate it. Thanks for your help. -- Best regards, Fabian F. Casteblanco Rutgers University -- Chemical Engineering PhD Student C: +908 917 0723 E: fabian.castebla...@gmail.com npt.mdp Description: Binary data md.mdp Description: Binary data -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Enthalpy of vaporization
Fabian Casteblanco wrote: Hello all, I am trying to find the enthalpy of vaporization for 7 types of alcohols to try to compare to experimental values. I have all of them simulated to equilibrium and I can use g_energy to view the Total Energy (both kinetic and potential). In order for me to find the enthalpy of vaporization, is it as simple as just running the NPT script again and changing the temperature to that of its boiling point and 1 degree K over that? Would it just be the difference between the enthalpy at boiling pt and 1 degree past boiling? If anyone could possibly lead me in the right direction I would greatly appreciate it. Thanks for your help. Use g_energy -nmol on your liquid state to extract potential energy per mole. Simulate one molecule in the gas phase (no PBC, all cutoffs equal to zero) and extract its potential energy. Then: DHvap = Epot(gas) - Epot(liq) + RT -Justin -- Best regards, Fabian F. Casteblanco Rutgers University -- Chemical Engineering PhD Student C: +908 917 0723 E: fabian.castebla...@gmail.com -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Invitation to connect on LinkedIn
LinkedIn srajan jain requested to add you as a connection on LinkedIn: -- Chinmay, I'd like to add you to my professional network on LinkedIn. - srajan Accept invitation from srajan jain http://www.linkedin.com/e/-85v1n9-gofphsu5-3b/Xl9gjr6GAOlB4vIjeR9gqTUPRTlBoITTu0/blk/I2857404434_2/1BpC5vrmRLoRZcjkkZt5YCpnlOt3RApnhMpmdzgmhxrSNBszYOnPgPd3gMd3sRe399bTBlqlB1u3xvbPsSdPAPcPkUc3cLrCBxbOYWrSlI/EML_comm_afe/ View invitation from srajan jain http://www.linkedin.com/e/-85v1n9-gofphsu5-3b/Xl9gjr6GAOlB4vIjeR9gqTUPRTlBoITTu0/blk/I2857404434_2/39vd3cQd30QdPkUcAALqnpPbOYWrSlI/svi/ -- (c) 2011, LinkedIn Corporation-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Fatal error: Not enough memory. Failed to realloc
Dear gmx-users, I was carrying out a continuation of an NPT equilibration from NVT. As soon the job started it ran into the following error: Fatal error: Not enough memory. Failed to realloc 1488624 bytes for nl-shift, nl-shift=0x0 (called from file ns.c, line 101) What is the error about? I did search few archives, in one someone had suggested to use an upgraded version. I am currently using 4.0.5 Is upgrading the solution to this problem? Thanks in advance, SN -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Protein ligand segmentation fault
Hi all, I have been trying to run a protein ligand simulation in water using Gromacs version 4.0.7 and GROMOS 53a6 ff. My protein is about 250 aa and my ligand is pip3 (Phosphatidylinositol (3,4,5)-trisphosphate) which I have constructed using PRODRG (using EM and full charges option). I have tried running the simulation several times under different conditions and every time the simulation crashed around the first few ps of MD giving a segmentation fault. I have tried coupling the temp and pressure of the ligand to the solvent and other times to the protein, changing the partial charges of the ligand using common GROMOS FF parametes. When running the same protein with a similar ligand (pip2) who's topology I have downloaded from the PDB website everything runs smoothly.. when running the protein and ligand in separate simulations they both run fine. I have also tried taking frames from the ligand and protein separate simulations and then placing them in the same box and still the simulation crashes. I have gone through Justin's tutorial on protein ligand simulations but to no avail. I'll be glad to provide further details to any one who think know what might be wrong.. Thanks, Gideon -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Protein ligand segmentation fault
גדעון לפידות wrote: Hi all, I have been trying to run a protein ligand simulation in water using Gromacs version 4.0.7 and GROMOS 53a6 ff. My protein is about 250 aa and my ligand is pip3 (Phosphatidylinositol (3,4,5)-trisphosphate) which I have constructed using PRODRG (using EM and full charges option). I have tried running the simulation several times under different conditions and every time the simulation crashed around the first few ps of MD giving a segmentation fault. I have tried coupling the temp and pressure of the ligand to the solvent and other times to the protein, changing the partial charges of the ligand using common GROMOS FF parametes. When running the same protein with a similar ligand (pip2) who's topology I have downloaded from the PDB website everything runs smoothly.. when running the protein and ligand in separate simulations they both run fine. I have also tried taking frames from the ligand and protein separate simulations and then placing them in the same box and still the simulation crashes. I have gone through Justin's tutorial on protein ligand simulations but to no avail. I'll be glad to provide further details to any one who think know what might be wrong.. Please post an .mdp file for a run that is crashing. Other general advice: http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System Since the simulation runs for a short time, you should be able to watch the trajectory and see where it starts to fall apart. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Enthalpy of Vaporization
Hello Justin, Thank you for your response. I just wanted to make sure I understand what you meant. I'm assuming that you want the one molecule in the gas phase at its boiling point and you are doing this because you want the molecule alone with no intermolecular interactions? (since heat of vaporization is the energy required to break those interactions amoung liquid molecules) Is that why we ignore kinetic energy? Is the liquid alcohol that I already simulated (liquid methanol, 1 bar, 298 K) also suppose to be at the 338 K boiling temperature? Would I simply run the npt equilibrium again but simply change the temperature from 298 to 338 K? Also, you stated the equation: DHvap = Epot(gas) - Epot(liq) + RT The first Epot(gas) would be the potential energy for 1 molecule but the Epot(liq) would be the potential energy for 1 mole? Thanks for your help Justin. -- Best regards, Fabian F. Casteblanco Rutgers University -- Chemical Engineering PhD Student C: +908 917 0723 E: fabian.castebla...@gmail.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Enthalpy of Vaporization
Fabian Casteblanco wrote: Hello Justin, Thank you for your response. I just wanted to make sure I understand what you meant. I'm assuming that you want the one molecule in the gas phase at its boiling point and you are doing this because you want the molecule alone with no intermolecular interactions? (since heat of vaporization is the energy required to break those interactions amoung liquid molecules) Is that why we ignore kinetic energy? Is the liquid alcohol that I already simulated (liquid methanol, 1 bar, 298 K) also suppose to be at the 338 K boiling temperature? Would I simply run the npt equilibrium again but simply change the temperature from 298 to 338 K? No, run both at the same temperature. Kinetic energy doesn't enter the equation here. Also, you need temperature to be constant in the equation below. If you run two simulations at two different temperatures, which T do you use. DHvap and other thermodynamic quantities are generally obtained at standard state, i.e. 298.15 K. Also, you stated the equation: DHvap = Epot(gas) - Epot(liq) + RT The first Epot(gas) would be the potential energy for 1 molecule but the Epot(liq) would be the potential energy for 1 mole? No, that's why you use g_energy -nmol for the liquid system. The output of g_energy is in kJ/mol of equivalent systems. Dividing by the value given in -nmol is energy in kJ/mol of molecules. That way, you compare the same quantities. Otherwise, you've got the energy of one molecule in the gas phase (kJ/mol of molecules) minus the energy of one mole of a system of molecules in the liquid phase (kJ/mol of systems). You'd get a nonsensical result. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_dipoles + tpbconv
Hello, I have a system with a glucose molecule. I want to calculate the dipole moment of a particular OH in glucose molecule.I made an index file which have a group containing atoms. [ O8 ] 8 18 10 is oxygen no. and 20 is hydroen no. But, if I try to use g_dipoles to get the dipole moment contribution from using following command: g_dipoles -f 6.trr -s 6.tpr -n index.ndx -corr mol -nonormalize -c I get the following error. Fatal error: index[1]=8 does not correspond to the first atom of a molecule I read on gmx-users mailing list. http://www.mail-archive.com/gmx-users@gromacs.org/msg40091.html Calculating a dipole moment of a possibly-charged species requires that there be a reference point, which is conventionally the center of mass of the molecule. This means all the atoms of the molecule have to be known, and g_dipoles assumes the index group consists of whole molecules. So to do the partition you want, you will need to provide the same molecules, but with zero charges. That will mean making a copy of your .top and hacking those charges to zero to generate a new such .tpr. Actually, tpbconv has the ability to set the charges of a group in a .tpr to zero. So I tried tpbconv -f 6.trr -s 6.tpr -n glu-emi-cl-128-no.ndx -e 6.edr -o zero.tpr I got the error segmentataion fault How can I solve this problem to calcualte the dipole moment of a bond? I am using gromacs version 4.0.7. Thanks Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] error: Only triclinic boxes...
Hello all,
I am getting the error below at the very beginning of the simulation (both
serial and parallel). I am sure I did not encounter this problem before with
the same input files. This has just happened now. I really have no clue why
this is happening. could you please help me? Thank you all in advance.
Warning: Only triclinic boxes with the first vector parallel to the x-axis
and the second vector in the xy-plane are supported.
Box (3x3):
Box[0]={ nan, 0.0e+00, 0.0e+00}
Box[1]={ nan, nan, nan}
Box[2]={ nan, nan, nan}
Can not fix pbc.
;Run control
integrator = md
dt = 0.002
nsteps = 100 ;5000
nstcomm = 100
;Output control
nstenergy = 100
nstxout = 100
nstvout = 0
nstfout = 0
nstlog = 1000
nstxtcout = 1000
;Neighbor searching
nstlist = 10
ns_type = grid
;Electrostatics/VdW
coulombtype = Shift
vdw-type= Shift
rcoulomb-switch = 0
rvdw-switch = 0.9 ;0
;Cut-offs
rlist = 1.25
rcoulomb= 1.0
rvdw= 1.0
;Temperature coupling
Tcoupl = v-rescale
tc-grps = System
tau_t = 0.1
ref_t = 300
;Pressure coupling
Pcoupl = Parrinello-Rahman
Pcoupltype = isotropic
tau_p = 1
compressibility = 3.5e-5
ref_p = 10
;Velocity generation
gen_vel = yes
gen_temp= 300.0
gen_seed= 173529
;Bonds
constraints = all-bonds
constraint-algorithm = lincs
--
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Re: [gmx-users] error: Only triclinic boxes...
Elisabeth wrote:
Hello all,
I am getting the error below at the very beginning of the simulation
(both serial and parallel). I am sure I did not encounter this problem
before with the same input files. This has just happened now. I really
have no clue why this is happening. could you please help me? Thank you
all in advance.
Warning: Only triclinic boxes with the first vector parallel to the
x-axis and the second vector in the xy-plane are supported.
Box (3x3):
Box[0]={ nan, 0.0e+00, 0.0e+00}
Box[1]={ nan, nan, nan}
Box[2]={ nan, nan, nan}
Can not fix pbc.
Your system is probably blowing up. Nan means not a number, so the box
vectors have become either infinitely large or small. Either the input
coordinate file contained a malformed or non-existent box, or the simulation is
collapsing along the way somewhere. Does the simulation run for a while before
printing this, or is it right away?
You can check the starting box vectors in the .tpr file with gmxdump to verify
that they are sensible.
-Justin
;Run control
integrator = md
dt = 0.002
nsteps = 100 ;5000
nstcomm = 100
;Output control
nstenergy = 100
nstxout = 100
nstvout = 0
nstfout = 0
nstlog = 1000
nstxtcout = 1000
;Neighbor searching
nstlist = 10
ns_type = grid
;Electrostatics/VdW
coulombtype = Shift
vdw-type= Shift
rcoulomb-switch = 0
rvdw-switch = 0.9 ;0
;Cut-offs
rlist = 1.25
rcoulomb= 1.0
rvdw= 1.0
;Temperature coupling
Tcoupl = v-rescale
tc-grps = System
tau_t = 0.1
ref_t = 300
;Pressure coupling
Pcoupl = Parrinello-Rahman
Pcoupltype = isotropic
tau_p = 1
compressibility = 3.5e-5
ref_p = 10
;Velocity generation
gen_vel = yes
gen_temp= 300.0
gen_seed= 173529
;Bonds
constraints = all-bonds
constraint-algorithm = lincs
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
--
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Re: [gmx-users] g_dipoles + tpbconv
Nilesh Dhumal wrote: Hello, I have a system with a glucose molecule. I want to calculate the dipole moment of a particular OH in glucose molecule.I made an index file which have a group containing atoms. [ O8 ] 8 18 10 is oxygen no. and 20 is hydroen no. I'm assuming you mean 8 is O and 18 is H? But, if I try to use g_dipoles to get the dipole moment contribution from using following command: g_dipoles -f 6.trr -s 6.tpr -n index.ndx -corr mol -nonormalize -c I get the following error. Fatal error: index[1]=8 does not correspond to the first atom of a molecule I read on gmx-users mailing list. http://www.mail-archive.com/gmx-users@gromacs.org/msg40091.html Calculating a dipole moment of a possibly-charged species requires that there be a reference point, which is conventionally the center of mass of the molecule. This means all the atoms of the molecule have to be known, and g_dipoles assumes the index group consists of whole molecules. So to do the partition you want, you will need to provide the same molecules, but with zero charges. That will mean making a copy of your .top and hacking those charges to zero to generate a new such .tpr. Actually, tpbconv has the ability to set the charges of a group in a .tpr to zero. So I tried tpbconv -f 6.trr -s 6.tpr -n glu-emi-cl-128-no.ndx -e 6.edr -o zero.tpr This command doesn't accomplish anything. If you're trying to zero out the charges, you need to use the -zeroq option. But then, if you have two atoms with zero charge, then the dipole will of course be zero! I got the error segmentataion fault How can I solve this problem to calcualte the dipole moment of a bond? I doubt you can do it with g_dipoles. You've been told already that the group analyzed has to have a net charge of zero. An OH group will not satisfy that need, nor does assigning each of the atoms zero charge. You're better off using g_dist (or maybe g_bond) to find the distance between the O and H atoms over time and plug that into an equation using the partial charges on the atoms to calculate the dipole yourself. The charges are fixed, so the only thing that changes (in the absence of constraints) is the distance between them. -Justin I am using gromacs version 4.0.7. Thanks Nilesh -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Re: question about trjcat command: Merge files
Dear community. Thanks to all, finally I could resolve my problem, with the option -setttime, it was vital, then c (continue). Now I have two questions, 1) In which case the option l could be useful? I did not understand very well the aplicability. 2) Could you please recommend me an article (Most cited maybe) or tutorial that analyze changes in protein folding due to single mutation? I would like to study its methodology. Thanks in advance. Miguel. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Enthalpy of Vaporization
Thanks Justin. That clarified a lot. I'm having trouble simulating the 1 molecule of gas methanol. I took the original energy minimized molecule and I'm trying to start it off on NVT using the following *.mdp file. I got rid of PBC (ns_type=simple) and I set rlist=infinite. After correcting some errors, Can not have dispersion correction with pbc=no, (set dispcorr=no), and setting nstlist=0 since Gromacs says simulating without cut-offs is usually faster with nstlist=0, I now keep getting an error saying Can not have nstlist=0 with twin-range interactions. Should nstlist be =0 as it says in the Gromacs manual when simulating with no cut-offs for pbc=no? It says I can not have Ewald with pbc=no which makes sense but I don't know what to replace it with. Thanks Justin. I appreciate your help. -- Best regards, Fabian F. Casteblanco Rutgers University -- Chemical Engineering PhD Student C: +908 917 0723 E: fabian.castebla...@gmail.com nvt.mdp Description: Binary data -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Enthalpy of Vaporization
Fabian Casteblanco wrote: Thanks Justin. That clarified a lot. I'm having trouble simulating the 1 molecule of gas methanol. I took the original energy minimized molecule and I'm trying to start it off on NVT using the following *.mdp file. I got rid of PBC (ns_type=simple) and I set rlist=infinite. After correcting some errors, Can not have dispersion correction with pbc=no, (set dispcorr=no), and setting nstlist=0 since Gromacs says simulating without cut-offs is usually faster with nstlist=0, I now keep getting an error saying Can not have nstlist=0 with twin-range interactions. Should nstlist be =0 as it says in the Gromacs manual when simulating with no cut-offs for pbc=no? It says I can not have Ewald with pbc=no which makes sense but I don't know what to replace it with. A few things: 1. rlist = infinite is not an option. The value of rlist is a floating-point number. To achieve infinite cutoffs, set rlist=rvdw=rcoulomb=0. 2. Don't use PME. Set coulombtype = cutoff. There are no cutoff artifacts here, since with rcoulomb=0, all interactions are calculated. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Switching from v4.0.7 to v 4.5.3 - being able to get the correct terms from a edr file when continuing a simulation
Hi, I'm doing a coarse-grained simulation, using the MARTINI forcefield, of a protein in a lipid bilayer. I carried out the equilibration stages using Gromacs 4.0.7. Equilibration was done in several stages but the last stage was with a Nosé-Hoover thermostat for temperature coupling and Parrinello-Rahman thermostat for pressure coupling. The next stage I carried out was a simulation of system with nothing except the backbone of the protein restrained, to relax the sidechains. For this stage I used a newer, faster server which has Gromacs 4.5.3 installed on it. The mdp file is below. I used the command: g_grompp -f ../md_T296.mdp -p ../prot_memb_system2.top -c npt_bPR.gro - e npt_bPR.edr -t npt_bPR.trr -n prot_bilayer.ndx -o md_schain I got the error message: --- Program g_grompp, VERSION 4.5.3 Source code file: /builddir/build/BUILD/gromacs-4.5.3/src/gmxlib/ enxio.c, line: 1056 Fatal error: Could not find energy term named 'Xi-0-Protein' For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I assumed that this was something to do with my switching between versions, maybe that the .edr file that's written by version 4.0.7 doesn't have the terms that are required by version 4.5.3, so I removed the -e option from the command line and ran the simulation using the commands: g_grompp -f ../md_T296.mdp -p ../prot_memb_system2.top -c npt_bPR.gro - t npt_bPR.trr -n prot_bilayer.ndx -o md_schain g_mdrun -v -nt 1 -deffnm md_schain For the next stage, I want to simulate the whole system, for which I use the mdp file below except with no -DPOSREBB defined (line 10) and with nsteps = 1000, and version 4.5.3 again. When I use the command: g_grompp -f ../md_T296.mdp -p ../prot_memb_system2.top -c md_schain.gro -e md_schain.edr -t md_schain.trr -n prot_bilayer.ndx -o md1_t296 I again get the error message: --- Program g_grompp, VERSION 4.5.3 Source code file: /builddir/build/BUILD/gromacs-4.5.3/src/gmxlib/ enxio.c, line: 1056 Fatal error: Could not find energy term named 'Xi-0-Protein' For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Can you help me with exactly what's going wrong? I'm not sure if I should be carrying out the simulation without being able to pass on the information from the .edr file of the sidechain-relaxing simulation? If not, what can I do to pass on the information necessary from the .edr file? Many thanks in advance, Anna *** mdp file *** ; ; STANDARD MD INPUT OPTIONS FOR MARTINI 2.0 ; ; for use with GROMACS 3.3 ; ; VARIOUS PREPROCESSING OPTIONS = title= Martini cpp = /usr/bin/cpp define = -DPOSREBB ; RUN CONTROL PARAMETERS = ; MARTINI - Most simulations are stable with dt=40 fs, ; some (especially rings) require 20-30 fs. ; The range of time steps used for parametrization ; is 20-40 fs, using smaller time steps is therefore not recommended. integrator = md ; start time and timestep in ps tinit= 0.0 dt = 0.030 nsteps = 100 ; number of steps for center of mass motion removal = nstcomm = 1 comm-mode= Linear comm-grps= Protein_Lipids W ; OUTPUT CONTROL OPTIONS = ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 5000 nstvout = 5000 nstfout = 0 ; Output frequency for energies to log file and energy file = nstlog = 1000 nstenergy= 1000 ; Output frequency and precision for xtc file = nstxtcout= 1000 xtc_precision= 100 ; This selects the subset of atoms for the xtc file. You can = ; select multiple groups. By default all atoms will be written. = xtc-grps = ; Selection of energy groups = energygrps = ; NEIGHBORSEARCHING PARAMETERS = ; MARTINI - no need for more frequent updates ; or larger neighborlist cut-off due ; to the use of shifted potential energy functions. ; nblist update frequency = nstlist = 10 ; ns algorithm (simple or grid) = ns_type = grid ; Periodic boundary conditions: xyz or none = pbc = xyz ; nblist cut-off = rlist= 1.2 ; OPTIONS FOR ELECTROSTATICS AND VDW = ; MARTINI - vdw and electrostatic interactions are used ; in their shifted forms. Changing to other types of ; electrostatics will affect
Re: [gmx-users] Switching from v4.0.7 to v 4.5.3 - being able to get the correct terms from a edr file when continuing a simulation
Anna Duncan wrote: Hi, I'm doing a coarse-grained simulation, using the MARTINI forcefield, of a protein in a lipid bilayer. I carried out the equilibration stages using Gromacs 4.0.7. Equilibration was done in several stages but the last stage was with a Nosé-Hoover thermostat for temperature coupling and Parrinello-Rahman thermostat for pressure coupling. The next stage I carried out was a simulation of system with nothing except the backbone of the protein restrained, to relax the sidechains. For this stage I used a newer, faster server which has Gromacs 4.5.3 installed on it. The mdp file is below. I used the command: g_grompp -f ../md_T296.mdp -p ../prot_memb_system2.top -c npt_bPR.gro -e npt_bPR.edr -t npt_bPR.trr -n prot_bilayer.ndx -o md_schain I got the error message: --- Program g_grompp, VERSION 4.5.3 Source code file: /builddir/build/BUILD/gromacs-4.5.3/src/gmxlib/enxio.c, line: 1056 Fatal error: Could not find energy term named 'Xi-0-Protein' For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I assumed that this was something to do with my switching between versions, maybe that the .edr file that's written by version 4.0.7 doesn't have the terms that are required by version 4.5.3, so I removed the -e option from the command line and ran the simulation using the commands: g_grompp -f ../md_T296.mdp -p ../prot_memb_system2.top -c npt_bPR.gro -t npt_bPR.trr -n prot_bilayer.ndx -o md_schain g_mdrun -v -nt 1 -deffnm md_schain For the next stage, I want to simulate the whole system, for which I use the mdp file below except with no -DPOSREBB defined (line 10) and with nsteps = 1000, and version 4.5.3 again. When I use the command: g_grompp -f ../md_T296.mdp -p ../prot_memb_system2.top -c md_schain.gro -e md_schain.edr -t md_schain.trr -n prot_bilayer.ndx -o md1_t296 I again get the error message: --- Program g_grompp, VERSION 4.5.3 Source code file: /builddir/build/BUILD/gromacs-4.5.3/src/gmxlib/enxio.c, line: 1056 Fatal error: Could not find energy term named 'Xi-0-Protein' For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- What does g_energy tell you is in the .edr file? If g_energy says Xi-0-Protein is present, but grompp can't find it, then perhaps there's a grompp-specific problem reading the energy file. It would also be interesting to know if the problem persists in 4.5.4, as I know there has been some debugging of .edr files, but I can't find anything specific in the release history that might be pertinent here. Can you help me with exactly what's going wrong? I'm not sure if I should be carrying out the simulation without being able to pass on the information from the .edr file of the sidechain-relaxing simulation? If not, what can I do to pass on the information necessary from the .edr file? Forget about passing .trr and .edr files to grompp. It's more accurate to simply pass a checkpoint file to grompp -t. Checkpoints contain all the necessary state information for the system. -Justin Many thanks in advance, Anna *** mdp file *** ; ; STANDARD MD INPUT OPTIONS FOR MARTINI 2.0 ; ; for use with GROMACS 3.3 ; ; VARIOUS PREPROCESSING OPTIONS = title= Martini cpp = /usr/bin/cpp define = -DPOSREBB ; RUN CONTROL PARAMETERS = ; MARTINI - Most simulations are stable with dt=40 fs, ; some (especially rings) require 20-30 fs. ; The range of time steps used for parametrization ; is 20-40 fs, using smaller time steps is therefore not recommended. integrator = md ; start time and timestep in ps tinit= 0.0 dt = 0.030 nsteps = 100 ; number of steps for center of mass motion removal = nstcomm = 1 comm-mode = Linear comm-grps = Protein_Lipids W ; OUTPUT CONTROL OPTIONS = ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 5000 nstvout = 5000 nstfout = 0 ; Output frequency for energies to log file and energy file = nstlog = 1000 nstenergy= 1000 ; Output frequency and precision for xtc file = nstxtcout= 1000 xtc_precision= 100 ; This selects the subset of atoms for the xtc file. You can = ; select multiple groups. By default all atoms will be written. = xtc-grps = ; Selection of energy groups = energygrps = ;
Re: [gmx-users] Switching from v4.0.7 to v 4.5.3 - being able to get the correct terms from a edr file when continuing a simulation
Hi Justin, Thanks for your speedy response. I've set off the simulation with the checkpoint file rather than the trajectory and energy files and that seems to be going fine now. v4.5.3 g_energy showed the .edr file from the backbone-restrained run to have no Xi-0-Protein term present, although the .edr file from the equilibration run has a term called 'Xi-Protein' Best wishes, Anna On 2 Jun 2011, at 18:36, Justin A. Lemkul wrote: Anna Duncan wrote: Hi, I'm doing a coarse-grained simulation, using the MARTINI forcefield, of a protein in a lipid bilayer. I carried out the equilibration stages using Gromacs 4.0.7. Equilibration was done in several stages but the last stage was with a Nosé-Hoover thermostat for temperature coupling and Parrinello-Rahman thermostat for pressure coupling. The next stage I carried out was a simulation of system with nothing except the backbone of the protein restrained, to relax the sidechains. For this stage I used a newer, faster server which has Gromacs 4.5.3 installed on it. The mdp file is below. I used the command: g_grompp -f ../md_T296.mdp -p ../prot_memb_system2.top -c npt_bPR.gro -e npt_bPR.edr -t npt_bPR.trr -n prot_bilayer.ndx -o md_schain I got the error message: --- Program g_grompp, VERSION 4.5.3 Source code file: /builddir/build/BUILD/gromacs-4.5.3/src/gmxlib/ enxio.c, line: 1056 Fatal error: Could not find energy term named 'Xi-0-Protein' For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I assumed that this was something to do with my switching between versions, maybe that the .edr file that's written by version 4.0.7 doesn't have the terms that are required by version 4.5.3, so I removed the -e option from the command line and ran the simulation using the commands: g_grompp -f ../md_T296.mdp -p ../prot_memb_system2.top -c npt_bPR.gro -t npt_bPR.trr -n prot_bilayer.ndx -o md_schain g_mdrun -v -nt 1 -deffnm md_schain For the next stage, I want to simulate the whole system, for which I use the mdp file below except with no -DPOSREBB defined (line 10) and with nsteps = 1000, and version 4.5.3 again. When I use the command: g_grompp -f ../md_T296.mdp -p ../prot_memb_system2.top -c md_schain.gro -e md_schain.edr -t md_schain.trr -n prot_bilayer.ndx -o md1_t296 I again get the error message: --- Program g_grompp, VERSION 4.5.3 Source code file: /builddir/build/BUILD/gromacs-4.5.3/src/gmxlib/ enxio.c, line: 1056 Fatal error: Could not find energy term named 'Xi-0-Protein' For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- What does g_energy tell you is in the .edr file? If g_energy says Xi-0-Protein is present, but grompp can't find it, then perhaps there's a grompp-specific problem reading the energy file. It would also be interesting to know if the problem persists in 4.5.4, as I know there has been some debugging of .edr files, but I can't find anything specific in the release history that might be pertinent here. Can you help me with exactly what's going wrong? I'm not sure if I should be carrying out the simulation without being able to pass on the information from the .edr file of the sidechain-relaxing simulation? If not, what can I do to pass on the information necessary from the .edr file? Forget about passing .trr and .edr files to grompp. It's more accurate to simply pass a checkpoint file to grompp -t. Checkpoints contain all the necessary state information for the system. -Justin Many thanks in advance, Anna *** mdp file *** ; ; STANDARD MD INPUT OPTIONS FOR MARTINI 2.0 ; ; for use with GROMACS 3.3 ; ; VARIOUS PREPROCESSING OPTIONS = title= Martini cpp = /usr/bin/cpp define = -DPOSREBB ; RUN CONTROL PARAMETERS = ; MARTINI - Most simulations are stable with dt=40 fs, ; some (especially rings) require 20-30 fs. ; The range of time steps used for parametrization ; is 20-40 fs, using smaller time steps is therefore not recommended. integrator = md ; start time and timestep in ps tinit= 0.0 dt = 0.030 nsteps = 100 ; number of steps for center of mass motion removal = nstcomm = 1 comm-mode = Linear comm-grps = Protein_Lipids W ; OUTPUT CONTROL OPTIONS = ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 5000 nstvout = 5000 nstfout
[gmx-users] Enthalpy of Vaporization
Thanks Justin. It worked and it is only off by 3% from experimental value so that is great. Thanks for your help! -- Best regards, Fabian F. Casteblanco Rutgers University -- Chemical Engineering PhD Student C: +908 917 0723 E: fabian.castebla...@gmail.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] error: Only triclinic boxes...
Hello Justin,
Thank you. I am using
gmxdump -s *.tpr -om to produce mdout.mdp file but I dont see box vector
information. This error happens at the very beginning. I see no steps are
calculated.
On 2 June 2011 13:11, Justin A. Lemkul jalem...@vt.edu wrote:
Elisabeth wrote:
Hello all,
I am getting the error below at the very beginning of the simulation (both
serial and parallel). I am sure I did not encounter this problem before with
the same input files. This has just happened now. I really have no clue why
this is happening. could you please help me? Thank you all in advance.
Warning: Only triclinic boxes with the first vector parallel to the x-axis
and the second vector in the xy-plane are supported.
Box (3x3):
Box[0]={ nan, 0.0e+00, 0.0e+00}
Box[1]={ nan, nan, nan}
Box[2]={ nan, nan, nan}
Can not fix pbc.
Your system is probably blowing up. Nan means not a number, so the box
vectors have become either infinitely large or small. Either the input
coordinate file contained a malformed or non-existent box, or the simulation
is collapsing along the way somewhere. Does the simulation run for a while
before printing this, or is it right away?
You can check the starting box vectors in the .tpr file with gmxdump to
verify that they are sensible.
-Justin
;Run control integrator = md
dt = 0.002 nsteps =
100 ;5000 nstcomm = 100
;Output control
nstenergy = 100nstxout = 100
nstvout = 0
nstfout = 0
nstlog = 1000 nstxtcout = 1000
;Neighbor searching
nstlist = 10 ns_type = grid
;Electrostatics/VdW
coulombtype = Shiftvdw-type=
Shift rcoulomb-switch = 0 rvdw-switch
= 0.9 ;0
;Cut-offs
rlist = 1.25 rcoulomb= 1.0
rvdw= 1.0
;Temperature coupling Tcoupl = v-rescale
tc-grps = System tau_t = 0.1
ref_t = 300 ;Pressure coupling
Pcoupl = Parrinello-RahmanPcoupltype
= isotropic tau_p = 1
compressibility = 3.5e-5 ref_p = 10
;Velocity generation gen_vel = yes
gen_temp= 300.0 gen_seed=
173529
;Bonds
constraints = all-bonds constraint-algorithm =
lincs
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
--
gmx-users mailing listgmx-users@gromacs.org
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--
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Re: [gmx-users] Switching from v4.0.7 to v 4.5.3 - being able to get the correct terms from a edr file when continuing a simulation
Anna Duncan wrote: Hi Justin, Thanks for your speedy response. I've set off the simulation with the checkpoint file rather than the trajectory and energy files and that seems to be going fine now. v4.5.3 g_energy showed the .edr file from the backbone-restrained run to have no Xi-0-Protein term present, although the .edr file from the equilibration run has a term called 'Xi-Protein' It looks like there may be a bug in the code, related to the nhchainlength parameter. The energy term names are now prefixed not by Xi- but Xi-(chain index), for which the only value can be zero, as I understand the code in its present form. I'll look into this a bit more and file a bug report, if necessary. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] error: Only triclinic boxes...
Elisabeth wrote:
Hello Justin,
Thank you. I am using
gmxdump -s *.tpr -om to produce mdout.mdp file but I dont see box
You don't need an mdout.mdp file, nor would box vectors be present in one. What
you're looking for is the box information present in the .tpr file. Run:
gmxdump -s topol.tpr out
Then search in the out file for the box information.
vector information. This error happens at the very beginning. I see no
steps are calculated.
Then the input box information is likely corrupt, or the simulation blows up at
the very start of the simulation (i.e. step 0).
-Justin
On 2 June 2011 13:11, Justin A. Lemkul jalem...@vt.edu
mailto:jalem...@vt.edu wrote:
Elisabeth wrote:
Hello all,
I am getting the error below at the very beginning of the
simulation (both serial and parallel). I am sure I did not
encounter this problem before with the same input files. This
has just happened now. I really have no clue why this is
happening. could you please help me? Thank you all in advance.
Warning: Only triclinic boxes with the first vector parallel to
the x-axis and the second vector in the xy-plane are supported.
Box (3x3):
Box[0]={ nan, 0.0e+00, 0.0e+00}
Box[1]={ nan, nan, nan}
Box[2]={ nan, nan, nan}
Can not fix pbc.
Your system is probably blowing up. Nan means not a number, so
the box vectors have become either infinitely large or small.
Either the input coordinate file contained a malformed or
non-existent box, or the simulation is collapsing along the way
somewhere. Does the simulation run for a while before printing
this, or is it right away?
You can check the starting box vectors in the .tpr file with gmxdump
to verify that they are sensible.
-Justin
;Run control integrator
= mddt = 0.002
nsteps = 100 ;5000 nstcomm
= 100
;Output control
nstenergy = 100nstxout =
100 nstvout = 0
nstfout = 0
nstlog = 1000 nstxtcout = 1000
;Neighbor searching
nstlist = 10 ns_type =
grid
;Electrostatics/VdW
coulombtype = Shiftvdw-type
= Shift rcoulomb-switch = 0
rvdw-switch = 0.9 ;0
;Cut-offs
rlist = 1.25 rcoulomb
= 1.0rvdw= 1.0
;Temperature coupling Tcoupl = v-rescale
tc-grps = System tau_t
= 0.1ref_t = 300
;Pressure coupling
Pcoupl = Parrinello-Rahman
Pcoupltype = isotropic tau_p
= 1 compressibility = 3.5e-5
ref_p = 10
;Velocity generation gen_vel =
yes gen_temp= 300.0
gen_seed= 173529
;Bonds
constraints = all-bonds
constraint-algorithm = lincs
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu http://vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
[gmx-users] Solvating dodecahedron
Hello All, I am trying to solvate a protein sitting in a dodecahedron using genbox. It gets solvated but a box of solvent is created around the protein. I want the protein to be sitting in a dodecahedron filed with solvent. I used the following commands: editconf -f onlyhis.gro -bt dodecahedron -box 9 -d 1 -o dodec.gro genbox -cp dodec.gro -cs mix.gro -o solv.gro I have never used this utility of creating a docecahedron nor I could find a way to view the dodecahedron shae in VMD. Am I going wrong? Thanks, SN -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] error: Only triclinic boxes...
Dear Justin,
I find:
box (3x3):
box[0]={ 1.6e+01, 0.0e+00, 0.0e+00}
box[1]={ 0.0e+00, 1.6e+01, 0.0e+00}
box[2]={ 0.0e+00, 0.0e+00, 1.6e+01}
box_rel (3x3):
box_rel[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
box_rel[1]={ 0.0e+00, 1.0e+00, 0.0e+00}
box_rel[2]={ 0.0e+00, 0.0e+00, 1.0e+00}
boxv (3x3):
boxv[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
boxv[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
boxv[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
pres_prev (3x3):
pres_prev[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
pres_prev[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
pres_prev[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
svir_prev (3x3):
svir_prev[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
svir_prev[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
svir_prev[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
fvir_prev (3x3):
fvir_prev[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
fvir_prev[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
fvir_prev[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
nosehoover_xi: not available
x (2896x3):
x[0]={-7.49400e+00, 4.57000e-01, 5.0e-01}
x[1]={-7.58200e+00, 5.21000e-01, 5.0e-01}
x[2]={-7.49600e+00, 3.94000e-01, 4.11000e-01}
x[3]={-7.49600e+00, 3.94000e-01, 5.89000e-01}
x[4]={-7.36800e+00, 5.43000e-01, 5.0e-01}
x[5]={-7.36800e+00, 6.06000e-01, 5.89000e-01}
x[6]={-7.36800e+00, 6.06000e-01, 4.11000e-01}
x[7]={-7.24200e+00, 4.57000e-01, 5.0e-01}
x[8]={-7.24200e+00, 3.94000e-01, 4.11000e-01}
x[9]={-7.24200e+00, 3.94000e-01, 5.89000e-01}
x[ 10]={-7.11700e+00, 5.43000e-01, 5.0e-01}
x[ 11]={-7.11700e+00, 6.06000e-01, 5.89000e-01}
x[ 12]={-7.11700e+00, 6.06000e-01, 4.11000e-01}
x[ 13]={-6.99100e+00, 4.57000e-01, 5.0e-01}
I made box bigger to remove bad contacts in initial configuration (although
I have been using the same gro file before and never got such error). Do you
recommend I reinstall 4.5.4 ?
Appreciate any help...
Regards,
On 2 June 2011 14:47, Justin A. Lemkul jalem...@vt.edu wrote:
Elisabeth wrote:
Hello Justin,
Thank you. I am using
gmxdump -s *.tpr -om to produce mdout.mdp file but I dont see box
You don't need an mdout.mdp file, nor would box vectors be present in one.
What you're looking for is the box information present in the .tpr file.
Run:
gmxdump -s topol.tpr out
Then search in the out file for the box information.
vector information. This error happens at the very beginning. I see no
steps are calculated.
Then the input box information is likely corrupt, or the simulation blows
up at the very start of the simulation (i.e. step 0).
-Justin
On 2 June 2011 13:11, Justin A. Lemkul jalem...@vt.edu mailto:
jalem...@vt.edu wrote:
Elisabeth wrote:
Hello all,
I am getting the error below at the very beginning of the
simulation (both serial and parallel). I am sure I did not
encounter this problem before with the same input files. This
has just happened now. I really have no clue why this is
happening. could you please help me? Thank you all in advance.
Warning: Only triclinic boxes with the first vector parallel to
the x-axis and the second vector in the xy-plane are supported.
Box (3x3):
Box[0]={ nan, 0.0e+00, 0.0e+00}
Box[1]={ nan, nan, nan}
Box[2]={ nan, nan, nan}
Can not fix pbc.
Your system is probably blowing up. Nan means not a number, so
the box vectors have become either infinitely large or small.
Either the input coordinate file contained a malformed or
non-existent box, or the simulation is collapsing along the way
somewhere. Does the simulation run for a while before printing
this, or is it right away?
You can check the starting box vectors in the .tpr file with gmxdump
to verify that they are sensible.
-Justin
;Run control integrator
= mddt = 0.002
nsteps = 100 ;5000 nstcomm=
100 ;Output control
nstenergy = 100nstxout =
100 nstvout = 0
nstfout = 0
nstlog = 1000 nstxtcout = 1000
;Neighbor searching
nstlist = 10 ns_type =
grid ;Electrostatics/VdW
coulombtype
[gmx-users] g_rdf: how to change grid spacing for structure factor
Hi, I am using gromacs_4.0.7 to calculate the Scattering Intensity as a function of scattering vectors(q) using g_rdf -sq command . But, I found that there is no way that one can increase/decrease the grid spacing for structure factor calculation. I tried using -bin option , but that does not change anything as that only works for changing bin-width for Radial distribution function calculation. If some one can point me out any way out of changing the grid spacing for structure factor, that will be very helpful. Sanku-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] error: Only triclinic boxes...
Elisabeth wrote:
Dear Justin,
I find:
box (3x3):
box[0]={ 1.6e+01, 0.0e+00, 0.0e+00}
box[1]={ 0.0e+00, 1.6e+01, 0.0e+00}
box[2]={ 0.0e+00, 0.0e+00, 1.6e+01}
box_rel (3x3):
box_rel[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
box_rel[1]={ 0.0e+00, 1.0e+00, 0.0e+00}
box_rel[2]={ 0.0e+00, 0.0e+00, 1.0e+00}
boxv (3x3):
boxv[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
boxv[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
boxv[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
pres_prev (3x3):
pres_prev[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
pres_prev[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
pres_prev[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
svir_prev (3x3):
svir_prev[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
svir_prev[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
svir_prev[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
fvir_prev (3x3):
fvir_prev[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
fvir_prev[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
fvir_prev[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
nosehoover_xi: not available
x (2896x3):
x[0]={-7.49400e+00, 4.57000e-01, 5.0e-01}
x[1]={-7.58200e+00, 5.21000e-01, 5.0e-01}
x[2]={-7.49600e+00, 3.94000e-01, 4.11000e-01}
x[3]={-7.49600e+00, 3.94000e-01, 5.89000e-01}
x[4]={-7.36800e+00, 5.43000e-01, 5.0e-01}
x[5]={-7.36800e+00, 6.06000e-01, 5.89000e-01}
x[6]={-7.36800e+00, 6.06000e-01, 4.11000e-01}
x[7]={-7.24200e+00, 4.57000e-01, 5.0e-01}
x[8]={-7.24200e+00, 3.94000e-01, 4.11000e-01}
x[9]={-7.24200e+00, 3.94000e-01, 5.89000e-01}
x[ 10]={-7.11700e+00, 5.43000e-01, 5.0e-01}
x[ 11]={-7.11700e+00, 6.06000e-01, 5.89000e-01}
x[ 12]={-7.11700e+00, 6.06000e-01, 4.11000e-01}
x[ 13]={-6.99100e+00, 4.57000e-01, 5.0e-01}
I made box bigger to remove bad contacts in initial configuration
(although I have been using the same gro file before and never got such
error). Do you recommend I reinstall 4.5.4 ?
Simply increasing a box size may not alleviate bad contacts in and of itself.
Plus, you're applying high pressure (10 bar), which is probably just causing the
box to rapidly collapse in on itself due to void space.
I doubt reinstalling would do any good. If your installation was severely
broken, nothing would be working.
-Justin
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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Re: [gmx-users] Solvating dodecahedron
shivangi nangia wrote: Hello All, I am trying to solvate a protein sitting in a dodecahedron using genbox. It gets solvated but a box of solvent is created around the protein. I want the protein to be sitting in a dodecahedron filed with solvent. I used the following commands: editconf -f onlyhis.gro -bt dodecahedron -box 9 -d 1 -o dodec.gro genbox -cp dodec.gro -cs mix.gro -o solv.gro I have never used this utility of creating a docecahedron nor I could find a way to view the dodecahedron shae in VMD. Am I going wrong? Nothing is wrong. The unit cell will always be in a triclinic representation. You can see a dodecahedron using trjconv -pbc mol -ur compact. Note that the pseudo-sphere representation is for visualization purposes only; the triclinic cell should be the input for any simulation. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Liquid/Gas Systems
Hi Justin, You had helped me earlier on calculating the heat of vaporization of methanol and it worked great. I'm just trying hard to understand conceptually what is the difference between simulating a liquid phase and a gas phase in Gromacs. I mean technically if we throw in 1000 molecules of component A, would it only be a gas if we made the box super huge? If we run NPT on a system, is that technically when we are compounding it together to find a liquid density? I'm just a bit confused on the difference. I've been simulating liquids up to this point so when I ran only NVT on a single gas molecule, I was trying to understand why we only run NVT on it (0 pressure so no pressure coupling). Thanks for your expertise. -- Best regards, Fabian F. Casteblanco Rutgers University -- Chemical Engineering PhD Student C: +908 917 0723 E: fabian.castebla...@gmail.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Liquid/Gas Systems
Fabian Casteblanco wrote: Hi Justin, You had helped me earlier on calculating the heat of vaporization of methanol and it worked great. I'm just trying hard to understand conceptually what is the difference between simulating a liquid phase and a gas phase in Gromacs. I mean technically if we throw in 1000 molecules of component A, would it only be a gas if we made the box super huge? If we run NPT on a system, is that technically when we are compounding it together to find a liquid density? I'm just a bit confused on the difference. I've been simulating liquids up to this point so when I ran only NVT on a single gas molecule, I was trying to understand why we only run NVT on it (0 pressure so no pressure coupling). The basic premise is that, in the gas phase, the gaseous species (atoms or molecules) do not interact (assuming an ideal gas), so yes, you absolutely could build a huge box that has N molecules in it to match your condensed phase system. What tends to happen is that molecules will eventually find one another and form clusters, which really (I think) is just an artifact of using condensed-phase parameters to simulate a gas. If the atoms/molecules find each other, they condense. This type of simulation would have to be done under NVT conditions, since gases fill the volume of their container, right? NPT would indeed just compress all of your particles together into a liquid. The purpose of simulating just a single molecule in isolation is that it easily satisfies all the requirements of the ideal state. The molecule is completely isolated and there are no periodicity artifacts. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] selecting atoms---MD analysis
Hi everyone! I have already have the MD data, I need to select certain atoms/residues with their XYZ coordinates in each time frame. I have problems in using the g_select if this is the proper tool to use for this. Thanks. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] selecting atoms---MD analysis
Mr Bernard Ramos wrote: Hi everyone! I have already have the MD data, I need to select certain atoms/residues with their XYZ coordinates in each time frame. I have problems in using the g_select if this is the proper tool to use for this. Thanks. g_select allows you to create dynamic indices, but the other analysis tools cannot yet make full use of the resulting index files. If the information you wish to extract is for a fixed set of atoms/residues, then use make_ndx and extract the desired coordinate information with g_traj. If this is not the case, then please provide additional details of what you wish to do and what exactly isn't working. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: compression to study pressure effect
Hey Eli:
What is the correlation observed between you and Moeed?
I suppose you eventually compressed your system so much, that it
became very distorted. Check your GRO file. I believe it is not
healthy inside.
Regards.
Dr. Vitaly V. Chaban, Department of Chemistry
University of Rochester, Rochester, New York 14627-0216
On Thu, Jun 2, 2011 at 6:53 PM, Moeed lecie...@googlemail.com wrote:
Dear Dr.Chaban,
I am so sorry to send you this message. Thank you for your comments. I have
encountered a problem that no one on the list could help much. I am very
hopeful you can assist me especially because I have noticed you respond to
messages dealing with compression or NPT runs. I am really confused since I
have been using the same input files (gro. top and mdp) and have been
collecting without any problem. Since yesterday I am getting a weird message
that is printed continuously until I kill mdrun.
arning: Only triclinic boxes with the first vector parallel to the x-axis
and the second vector in the xy-plane are supported.
Box (3x3):
Box[ 0]={ nan, nan, nan}
Box[ 1]={ nan, nan, nan}
Box[ 2]={ nan, nan, nan}
I have only polyethylene chains in my system. I really appreciate if you
could help me or could kindly take a very brief look at my system. I can
send you top and gro files. I assure you top file is generated properly. I
have done many runs using that. Please let me know if you are interested.
I thank you so much
Waiting for your reply.
Best regards,
Eli.
; Run control
integrator = md
dt = 0.002
nsteps = 100 ;5000
nstcomm = 100
; Output control
nstenergy = 100
nstxout = 100
nstvout = 0
nstfout = 0
nstlog = 1000
nstxtcout = 1000
; Neighbor searching
nstlist = 10
ns_type = grid
; Electrostatics/VdW
coulombtype = Shift
vdw-type = Shift
rcoulomb-switch = 0
rvdw-switch = 0.9 ;0
; Cut-offs
rlist = 1.25
rcoulomb = 1.0 ;1.1
rvdw = 1.0
; Temperature coupling
Tcoupl = v-rescale
tc-grps = System ;HEX
tau_t = 0.1 ;0.1
ref_t = 300 ;300
; Pressure coupling
Pcoupl = Parrinello-Rahman
Pcoupltype = isotropic
tau_p = 1 ;0.5
compressibility = 4.5e-5 4.5e-5
ref_p = 10 30
; Velocity generation
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529
; Bonds
constraints = all-bonds
constraint-algorithm = lincs
On 1 June 2011 14:59, Vitaly Chaban vvcha...@gmail.com wrote:
Either a tighter pressure coupling time...
On Wed, Jun 1, 2011 at 2:57 PM, Vitaly Chaban vvcha...@gmail.com wrote:
Hmm...
1. The background of the task is not quite clear for me.
2. Evidently, the fluctuations are higher than the difference for your
pressures.
3. Why not to use significantly larger systems and significantly
larger difference between pressures?
--
Dr. Vitaly V. Chaban, Department of Chemistry
University of Rochester, Rochester, New York 14627-0216
I am trying to study the effect of pressure on total potential of my
system
(8 polymer chains). My problem is that I dont see a systematic effect
of
pressure on potentials and I cant judge if different pressures increase
or
decrease potential. This is the critical observable in my system and
with
high fluctuations I am getting I cant make comment on pressure effect.
Total
drift is high in most potential functions..I start my runs from a frame
which is the output of an older NPT run (I use cpt file) that has a
close
density to what I want. In the production runs (NPT for 12 27 70 bar).
Below is the settings I am using and I really appreciate it if you
could
comment on the most important factors for such a study. I tried
different
cutoffs as well...I though maybe increasing cutoffs invloves more
interactions and can represent better the pressure effect...
Thanks so much!
; Run control
integrator = md
dt = 0.002
nsteps = 100 ;5000
nstcomm = 100
; Output control
nstenergy = 100
nstxout = 100
nstvout = 0
nstfout = 0
nstlog = 1000
nstxtcout = 1000
; Neighbor searching
nstlist = 10
ns_type = grid
; Electrostatics/VdW
coulombtype = Shift
vdw-type = Shift
rcoulomb-switch
[gmx-users] Re: Liquid/Gas Systems
You had helped me earlier on calculating the heat of vaporization of methanol and it worked great. I'm just trying hard to understand conceptually what is the difference between simulating a liquid phase and a gas phase in Gromacs. I mean technically if we throw in 1000 molecules of component A, would it only be a gas if we made the box super huge? If we run NPT on a system, is that technically when we are compounding it together to find a liquid density? I'm just a bit confused on the difference. I've been simulating liquids up to this point so when I ran only NVT on a single gas molecule, I was trying to understand why we only run NVT on it (0 pressure so no pressure coupling). I would say the things are much easier than you try to understand them. There is no difference between simulating different phases in MD at all. Generally, you may try NPT to simulate gaseous phase. BUT: you should start from already equilibrated gas phase, since barostats do not perform adequately if the pressure/volume drift a lot during MD. This is not a problem of MD itself. Dr. Vitaly V. Chaban, Department of Chemistry University of Rochester, Rochester, New York 14627-0216 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: compression to study pressure effect
Elisabeth wrote:
Hello Dr. Vitaly Chaban,
Thank you. I asked a friend in our Dept. for help who is working on
different aspects of the more or less similar system. The message below
was sent on behalf of me. I apologize if I should not have done this. We
thought maybe it does not matter under which name messages are sent on
the gmx list and the idea of using mailing list is to share knowledge
regardless of names. I hope this has not offended you and other users.
I am also asking Justin to let me know if I have violated mailing list
rules. I make sure this will not happen again.
http://www.gromacs.org/Support/Mailing_Lists#Mailing_List_Etiquette
Having others send information around haphazardly to different individuals and
from colleagues or aliases just slows down your overall progress, since we don't
know who's getting (or providing) what information, or if the discussions are
even connected. Keep everything on the list and reply directly to questions
posed to you with as much detail as you can.
It's also not a good idea for anyone to complain that no one on the list could
help much. I had been trying to extract the necessary diagnostic information
from you, but perhaps not at the pace you'd like. Problems aren't solved
instantly, especially via email by people who have only a very vague idea of
what you're doing.
-Justin
Thank you,
Best regards,
On 2 June 2011 21:03, Vitaly Chaban vvcha...@gmail.com
mailto:vvcha...@gmail.com wrote:
Hey Eli:
What is the correlation observed between you and Moeed?
I suppose you eventually compressed your system so much, that it
became very distorted. Check your GRO file. I believe it is not
healthy inside.
Regards.
Dr. Vitaly V. Chaban, Department of Chemistry
University of Rochester, Rochester, New York 14627-0216
On Thu, Jun 2, 2011 at 6:53 PM, Moeed lecie...@googlemail.com
mailto:lecie...@googlemail.com wrote:
Dear Dr.Chaban,
I am so sorry to send you this message. Thank you for your
comments. I have
encountered a problem that no one on the list could help much. I
am very
hopeful you can assist me especially because I have noticed you
respond to
messages dealing with compression or NPT runs. I am really
confused since I
have been using the same input files (gro. top and mdp) and have been
collecting without any problem. Since yesterday I am getting a
weird message
that is printed continuously until I kill mdrun.
arning: Only triclinic boxes with the first vector parallel to
the x-axis
and the second vector in the xy-plane are supported.
Box (3x3):
Box[0]={ nan, nan, nan}
Box[1]={ nan, nan, nan}
Box[2]={ nan, nan, nan}
I have only polyethylene chains in my system. I really appreciate
if you
could help me or could kindly take a very brief look at my
system. I can
send you top and gro files. I assure you top file is generated
properly. I
have done many runs using that. Please let me know if you are
interested.
I thank you so much
Waiting for your reply.
Best regards,
Eli.
;Run control
integrator = md
dt = 0.002
nsteps = 100 ;5000
nstcomm = 100
;Output control
nstenergy = 100
nstxout = 100
nstvout = 0
nstfout = 0
nstlog = 1000
nstxtcout = 1000
;Neighbor searching
nstlist = 10
ns_type = grid
;Electrostatics/VdW
coulombtype = Shift
vdw-type= Shift
rcoulomb-switch = 0
rvdw-switch = 0.9 ;0
;Cut-offs
rlist = 1.25
rcoulomb= 1.0 ;1.1
rvdw= 1.0
;Temperature coupling
Tcoupl = v-rescale
tc-grps = System ;HEX
tau_t = 0.1 ;0.1
ref_t = 300 ;300
;Pressure coupling
Pcoupl = Parrinello-Rahman
Pcoupltype = isotropic
tau_p = 1;0.5
compressibility = 4.5e-5 4.5e-5
ref_p = 1030
;Velocity generation
gen_vel = yes
gen_temp= 300.0
gen_seed= 173529
;Bonds
constraints = all-bonds
constraint-algorithm = lincs
On 1 June 2011
[gmx-users] option -pbc in trjconv
Dear users, I wanted to ensure that the option of -pbc in trjconv is only for visualization, and if I do all possible calculations with the original .xtc file there wont be any problem. Thank you With regards M. Kavyashree -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
