[gmx-users] g_dipole ? =>salt-molecule => Does Gromacs consider counter ions?

Hi When I issued the command g_dipole, the dialog poped out and asked me to select a group. 1. system 2. protein . 11. solvent 12. the rest of the salt-molecule except its counter ion 13. counter ions (CL-) If I select #12, Gromacs will not consider counter ions to calculate the di

[gmx-users] g_dipole ? =>salt-molecule => Does Gromacs consider counter ions?

-) If I select #12, Gromacs will not consider counter ions to calculate the dipole moment ??? Sorry for disturbing people in the Gromacs mailing list. Thank you Lin On 2010-10-22 00.49, Chih-Ying Lin wrote: > Hi > When I issued the command g_dipole, > the dialog poped out and asked me

[gmx-users] g_rmsf -res => average over time for each residue?

Hi g_rmsf -f abc.xtc -s abc.tpr -res -o abcrmsf.xvg *-[no]res* bool no Calculate averages for each residue abcrmsf.xvg => average over time for each residue? Thank you Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please sea

[gmx-users] g_rmsf -res => does Gromacs do average over time for each residue ?

Hi g_rmsf -f abc.xtc -s abc.tpr -res -o abcrmsf.xvg From manual => it says " Calculate averages for each residue " => does Gromacs do average over time for each residue ? => however, the results did not show difference with and without " -res "

[gmx-users] g_rmsf -res => what does this function work?

Hi >From Manual http://manual.gromacs.org/current/online/g_rmsf.html g_rmsf => optiontypedefaultdescription -[no]res bool noCalculate averages for each residue what does this function work? Thank you Lin -- gmx-users mailing listgmx-use

[gmx-users] g_rmsf -res yes ? => should I type "yes" to activate the "average-function" ?

Hi g_rmsf -res yes ? g_rmsf -res no ? should I type "yes" to activate the "average-function"? As i tested "g_rmsf -res", the average is not over time and not over the atoms in the residue. Anyway, how to activate the "average function" ? Thank you

[gmx-users] g_rmsf => average over # of time frames ???

Hi >From source code => gmx_rmsf.c "g_rmsf computes the root mean square fluctuation (RMSF, i.e. standard ", "deviation) of atomic positions ", if (devfn) { /* Calculate RMS Deviation */ for(i=0;(i-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.or

[gmx-users] High Temperature 498 K, NVT or NTP ?

Hi At high temperature 498 K, the protein is cooked. For NVT, the volume of the system is much expanded. For NPT, the water evaporated. How do people simulate the condition under high temperature, 498K? THank you Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/ma

[gmx-users] Standard Procedures to perform MD under High Temperature 498 K, either NVT or NTP ?

Hi I read some papers and many simulations were performed under high temperature to induce the unfolded protein. However, the authors did not mention how they conducted the simulations under high temperature, 498 K. They did not mention which NVT or NPT were adopted for such high temperature. None

[gmx-users] ZN2+ qtot 1.233e-06 ?

Hi I issued "pdb2gmx with G45a3 force field" on the "bovine carbonic anhydrase" >From the .top value, the ZN+2 is given qtot 1.233e-06 .. 2611 ZN2+257 ZN ZN 1137 2 65.37 ; qtot 1.233e-06 I am confused with the charges. Isn't ZN+2 carrying +2 charges ??

[gmx-users] ZN2+ qtot 1.233e-06 ?

Hi I issued "pdb2gmx with G45a3 force field" on the "bovine carbonic anhydrase" From the .top value, the ZN+2 is given qtot 1.233e-06 .. 2611 ZN2+257 ZN ZN 1137 2 65.37 ; qtot 1.233e-06 I am confused with the charges. Isn't ZN+2 carrying +2 cha

[gmx-users] Is the time scale of the protein domain motion within nano-second?

Hi Is the time scale of the protein domain motion within nano-second? Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before

[gmx-users] Long Simulation Time

HI i was reading somewhere.. "simulation will break / terminate when the simulation is running so so long "... Did anyone read the same information? Please refer me the related information since I have no idea where I read this information. How long is long ? How to avoid this? Thank

[gmx-users] Increase temperature to 550K

HI The simulation system is merely water + one lysozyme. I increase temperate to 550K. Then, the simulation broke. The following message is shown. MX:hpc0011:Remote endpoint is closed, peer=00:60:dd:48:14:5b (hpc0010:0) mpiexec: Warning: task 0 exited with status 1. mpiexec: Warning: tasks 1-2 di

[gmx-users] Increase temperature to 550K

lincs-iter = 1 lincs-warnangle = 30 Chih-Ying Lin wrote: > HI > The simulation system is merely water + one lysozyme. > I increase temperate to 550K. > > Then, the simulation broke. > The following message is shown. > > MX:hpc0011:Remote endpoint is

[gmx-users] Increase temperature to 550K

Hi the water model is TIP3P. Thanks Lin I think the problem is hidden in your water force field model. > The simulation system is merely water + one lysozyme. > I increase temperate to 550K. > > Then, the simulation broke. > The following message is shown. > > MX:hpc0011:Remote endpoint is cl

[gmx-users] Increase temperature to 550K

other methodological concerns (pressure coupling especially); a thorough search of the literature will give you some insights into what might be wrong. Plenty of groups have successfully been doing high-temperature MD for a number of years. -Justin Chih-Ying Lin wrote: > > Hi > the wa

[gmx-users] Increase temperature to 550K => simulation techniques ?

e you some insights into what might be wrong. Plenty of groups have successfully been doing high-temperature MD for a number of years. -Justin Chih-Ying Lin wrote: > > Hi > the water model is TIP3P. > > Thanks > Lin > > > > I think the problem is hidden in your wa

[gmx-users] Decreasing MSD of ligand ?

HI MSD = mean square displacement diffusion coefficient = d/dt (MSD) I simulate the protein and ligand system and then calculate the MSD of the ligand. Then, i drew the plot of the time evolution of the MSD. But the the MSD decreases as time for some period. I see nothing about my codings. Would yo

[gmx-users] Decreasing MSD of ligand ?

Hi The MSD decrease occurs in the long times. The ligand has bounded to a protein. How can the decrease happen? Thank you Lin Chih-Ying Lin wrote: > > > > HI MSD = mean square displacement diffusion coefficient = d/dt (MSD) I > simulate the protein and ligand system and the

[gmx-users] g_msd => The MSD and periodic boundary condition

Hi With the periodic boundary condition, all the recorded coordinates of the atom are within the simulation box. To calculate the MSD, the movement of the center mass of the molecules between this time step with the next time step is calculated without considering the periodic boundary condition. B

[gmx-users] How to put more solutes into the system ?

Hi I have a system - solutes with water. The system has been under MD simulation for 100 ns. Now, I want to put more solutes in it. Would you please tell me which command can make it ? Thank you Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-

[gmx-users] How to put more solutes into the system ?

ystem pbc = xyz (minim.mdp) => the system is crystallized with visualization 7. Relaxation of solvent and hydrogen atom positions Run => Position restrained MD => simulation break What is wrong here? How to put another 10 ligands into the simulation box correctly? Thank

[gmx-users] How to put more solutes into the system ?

system pbc = xyz (minim.mdp) => the system is crystallized with visualization 7. Relaxation of solvent and hydrogen atom positions Run => Position restrained MD => simulation break What is wrong here? How to put another 10 ligands into the simulation box correctly? Thank you

[gmx-users] some molecule clashing with another ?

Hi My simulation broke down and the simulation procedues are as follows. 1. center a protein molecule in the simulation box 2. put 20 ligands around the protein with " genbox " command 3. make sure that any atom of the ligands does not overlap on any atom of the protein with Visulization-software

[gmx-users] some molecule clashing with another ?

previous and current coordinates Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates Back Off! I just backed up step0.pdb to ./#step0.pdb.6# Wrote pdb files with previous and current coordinates Terminated Chih-Ying Lin wrote: > > > Hi

[gmx-users] How to modify or avoid some molecule clashing with another ?

From: "Justin A. Lemkul" Subject: Re: [gmx-users] some molecule clashing with another ? To: Discussion list for GROMACS users Message-ID: <4b3be9b3.8020...@vt.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Chih-Ying Lin wrote: > > > Hi > My simulation b

[gmx-users] some molecule clashing with another ?

--- Potential8.98118e+08 4.53312e+08 0 -3.03617e+07 -1.97304e+09 Kinetic En. 0 0 0 0 0 Total Energy 8.98118e+08 4.53312e+08 0 -3.03617e+07 -1.97304e+09 gcq#119: "Bring Out the Gimp" (Pulp Fiction) Chi

[gmx-users] LINCS WARNING max 597108032.000000 (between atoms 366 and 368) ?

Hi what does the max max 597108032.00 (between atoms 366 and 368) mean? is it the max force or max length of the system? where is the max force listed? max 597108032.00 (between atoms 366 and 368) rms 26394490.00 bonds that rotated more than 30 degrees: what does previous, current mean

[gmx-users] clashing happened inside the protein molecule?

Hi Here is my .out file. atoms 366 and 368 are two atoms inside the protein. What is other possible way to solve it ? Thank you Lin relative constraint deviation after LINCS: max 597108032.00 (between atoms 366 and 368) rms 26394490.00 bonds that rotated more than 30 degrees: atom 1

[gmx-users] Break ? => Position restrained MD

Hi In the position restrain MD, only solvent molecules and hydrogen atoms are allowed to move. I checked the .out file. The max is happened on the atoms inside protein. Why? Thank you Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Pleas

[gmx-users] Simulation Break => Due to bad domain decomposition ? (MPI) => Gromacs Version 3.3.3

Hi I used Gromacs version 3.3.3. My simulation system = one protein + 20 ligand + water molecules ( 7x 7x 7 ) MPI setting => #PBS -l nodes=4:ppn=4,arch=x86_64 => 16 nodes in total After doing the energy minimization, => the potential energy is extremely high ( say, ten to the 9th order ) I visual

[gmx-users] Simulation Box break into 16 domains => Gromacs 3.3.3

> > Hi > I used Gromacs version 3.3.3. > My simulation system = one protein + 20 ligand + water molecules ( 7x 7x 7 > ) > MPI setting => #PBS -l nodes=4:ppn=4,arch=x86_64 => 16 nodes in total > After doing the energy minimization, => the potential energy is extremely > high ( say, ten to the 9th

[gmx-users] Simulation Box break into 16 domains => Gromacs 3.3.3

Hi I used Gromacs version 3.3.3. My simulation system = one protein + 20 ligand + water molecules ( 7x 7x 7 ) MPI setting => #PBS -l nodes=4:ppn=4,arch=x86_64 => 16 nodes in total After doing the energy minimization, => the potential energy is extremely high ( say, ten to the 9th order ) I visua

[gmx-users] Simulation Box break into 16 domains => Gromacs 3.3.3

Hi Sorry that i have posted the same message for several times. I used Gromacs version 3.3.3. My simulation system = one protein + 20 ligand + water molecules ( 7x 7x 7 ) MPI setting => #PBS -l nodes=4:ppn=4,arch=x86_64 => 16 nodes in total After doing the energy minimization, => the potential e

[gmx-users] Gromacs 3.3.3 => what MPI based on ?

Hi There is no domain decomposition with Gromacs 3.3.3. What MPI based on with Gromacs 3.3.3? Thank you Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don'

[gmx-users] Simulation Box break into 16 domains => Gromacs 3.3.3

A. Lemkul" Subject: Re: [gmx-users] Simulation Box break into 16 domains => Gromacs 3.3.3 To: Discussion list for GROMACS users Message-ID: <4b3e8b11.7040...@vt.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Mark Abraham wrote: > Chih-Ying Lin wrote: >> &g

[gmx-users] Simulation Box break into 16 domains => Gromacs 3.3.3

is no description in the manual that people cannot use -d and -box simultaneously. I visualized the .gro file created by the editconf, the protein is centered in the box as I can see. Thank you Lin Chih-Ying Lin wrote: > > > > Hi > As I posted the command list earlier, to create t

[gmx-users] Simulation Box break into 16 domains => .tpr file is wrong (Gromacs 3.3.3)

-grompp.gro* *6LYZ-solvated.gro => all molecules are intact * and protein is centered. *6LYZ-EM-solvated-after-grompp.gro => protein and water molecules are broken.* ** ** This is the main problem that my simulation box into 16 domains. Thank you Lin ** ** ** Chih-Ying Lin wrote: > >

[gmx-users] Simulation Box break into 16 domains => .tpr file is wrong (Gromacs 3.3.3)

Hi, Thanks a lot, Tsjerk ! My simulation is running. I never knew that a discrepancy between the the .top file and .gro, grompp uses the topology information in stead of the coordinate file information. What does issue a set of warnings by grompp ? How do you know the discrepancy between the th

[gmx-users] low concentration simulation ?

HI I am simulating the protein + ligand + water molecules system. In the experimental work, the concentration of ligand is pretty low, say under 20 mM (avearge 18 ligands attached on one protein) It will be a huge system to create a system with 20 mM and it will take lot of simulation time. Inste

[gmx-users] low concentration simulation ?

the same way as if you add ten at a time? Will they aggregate? Will they inherently bind the protein in the same way, or will it be different? " => I don't know, but I assume that will make little difference. Thank you Lin Chih-Ying Lin wrote: > > HI > I am simulati

[gmx-users] simulation broke at 4.0.5 version

Hi I am using Gromacs version 4.0.5. I put one protein in a simulation box with water molecules and CL- only. My simulation broke at the step, Relaxation of solvent and hydrogen atom position. Here are the .top file, command, output of the grommp, pr.mdp. anything wrong here? Thank you Lin *[

[gmx-users] 6LYZ.pdb + Gromacs version 4.0.5 => Simulation Broken

Hi 6LYZ.pdb is simply a lysozyme structure and I merely solvated it running the simulation on Gromacs. System = 6LYZ.pdb + CL- + water molecules Before I put the 6LYZ.pdb on Gromacs 3.3.3, there is no problem at all. Recently, I tried the Gromacs 4.0.5, the simulation is broken at the step Positio

[gmx-users] 6LYZ.pdb + Gromacs version 4.0.5 => Simulation Broken (output file)

Hi 6LYZ.pdb is simply a lysozyme structure and I merely solvated it running the simulation on Gromacs. System = 6LYZ.pdb + CL- + water molecules Before I put the 6LYZ.pdb on Gromacs 3.3.3, there is no problem at all. Recently, I tried the Gromacs 4.0.5, the simulation is broken at the step Positio

[gmx-users] 6LYZ.pdb + Gromacs version 4.0.5 => Simulation Broken

Hi I did the EM and the potential energy went to the very negative number. But the simulaiton broke in the PR step. Thank you Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search befor

[gmx-users] 6LYZ.pdb + Gromacs version 4.0.5 => Simulation Broke

with the addition of ions to your .top file. In your protocol, it's not mentioned. Have you made sure that issue is cleared? Cheers, Tsjerk On Sun, Jan 10, 2010 at 5:25 AM, Justin A. Lemkul wrote: > > > On 1/9/10 10:42 PM, Chih-Ying Lin wrote: >> >> Hi >> I

[gmx-users] 6LYZ.pdb + Gromacs version 4.0.5 => Simulation Broken

Today's Topics: 1. 6LYZ.pdb + Gromacs version 4.0.5 => Simulation Broken (Chih-Ying Lin) 2. 6LYZ.pdb + Gromacs version 4.0.5 => Simulation Broken (output file) (Chih-Ying Lin) -- Message: 1 Date:

[gmx-users] grompp - commands

Hi Here are four commands. PART I grompp_mpi -np 16 -v -f md.mdp -c 6LYZ-MD.gro -p 6LYZ.top -o 6LYZ-MD55.tpr mpiexec -np 16 mdrun_mpi -deffnm 6LYZ-MD55 PART II grompp_mpi -np 16 -v -f md.mdp -c 6LYZ-MD55.gro -p 6LYZ.top -o 6LYZ-MD155.tpr mpiexec -np 16 mdrun_mpi -deffnm 6LYZ-MD155 Will t

[gmx-users] PH 5.0 ?

HI How to assign charge for the residue of protein at PH 5.0 ? I have Ka values of each residue of protein then i can calculate the overall charge for each residue at PH 5.0 solution. However, how to calculate the partial charges of atoms within the residue of protein at PH 5.0? Thank you Lin --

[gmx-users] Backbone and MainChain

Hi >From Gromacs Manual: - Backbone: all protein backbone atoms (C-alpha, N, C) - MainChain: backbone atoms, plus the carbonyl oxygens The following is part of .gro file. I listed the atom number, are those all correct ? C-alpha: 161,170,179 N:158,163, 172 C: ??? what does this "C" rep

[gmx-users] trjcat and trjconv

Hi file1.xtc and file2.xtc are two consecutive MD trajectory files of the same simulation system. file1.xtc = 238 frames (t= 0.0 to t= 476.0) file2.xtc = 366 frames (t= 0.0 to t= 732.0) trjcat -f file1.xtc file2.xtc -cat -o file3.xtc file3.xtc = 604 frames =23

[gmx-users] g_sas

Hi The command g_sas => Select a group for calculation of surface and a group for output What is the difference between "a group for calculation of surface" and "a group for output"? Thank you Lin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-us

[gmx-users] DSSP => how to edit .eps file

HI After running DSSP, .eps files are created. We can see the second structures of the all residues. I only want to see the change of the second structures of some specific residues. How can i do it? Also, how can I change the thickness of the color band for each residue? The logo indicates the co

[gmx-users] DSSP=> how to edit .eps file

HI 1. dssp -n index.ndx => only atom numbers of one residue in the index.ndx => can dssp decide the exact second structure for the only one residue without considering other residues of protein? => can i get the same second structure for the residue with [ dssp -n one-residue.ndx ] and [dssp -n p

[gmx-users] g_sas

HI THe command => g_sas_mpi -f 6LYZ-MD566500.xtc -s 6LYZ-MD566500.tpr -o solvent-accessible-surface.xvg -oa atomic-sas.xvg -or residue-sas.xvg In the solvent-accessible-surface.xvg => @ s0 legend "Hydrophobic" @ s1 legend "Hydrophilic" @ s2 legend "Total" @ s3 legend "D Gsolv" What does "Hydrop

[gmx-users] DSSP=> how to edit .eps file

Hi With the following two commands, do_dssp -f 6LYZ-MD.xtc -s 6LYZ-MD.tpr -o secondary-structure.xpm -sc secondary-structure.xvg xpm2ps -f secondary-structure.xpm -o secondary-structure.eps With GIMP, i can see the secondary structure plot. The legend indicates the color of different second str

[gmx-users] g_sas

Hi g_sas computes hydrophobic, hydrophilic and total solvent accessible surface area. I chose => protein for calculation group => protein for output group what does it define "hydrophobic solvent accessible surface area"? => does that, the surface area, enclose the hydrophobic atoms/

[gmx-users] g_sas

Hi >From David, "If you select a group consisting of a single residue in a protein the SAS will be computed as if the rest of the protein is not there. Very useful when you want to compute protein-protein interface areas." => therefore, if i select a group consisting of a single residue, which is

[gmx-users] DSSP=> how to edit .eps file

HI How to pass an .m2p file to xpm2ps to change the dimensions of the plot, data point size, etc. ??? Thank you Lin Chih-Ying Lin wrote: > > Hi > With the following two commands, > > do_dssp -f 6LYZ-MD.xtc -s 6LYZ-MD.tpr -o secondary-structure.xpm -sc secondary-structure.xv

[gmx-users] how many water molecule used to run MD?

Hi how many water molecules used to run MD? what is the criteria for this? I found some water.gro including 216 or 512 water molecules. Is it enough to include 216 or 512 water molecules only in MD system? For TIP4P; there are 4 coordinates to determine a water molecule. For TIP5P; there are

[gmx-users] TIP4P and TIP5P

Hi Could anyone tell me how to construct the solvent box of TIP4P and TIP5P model? And, how to construct water_TIP4P.itp and and water_TIP5P.itp ? Thank you very much Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailm

[gmx-users] Re: how many water molecule used to run MD?

Hi Would you please explain "the short-range potential saturated"? What is the short-range potential? Also, how to measure the short-range potential? Thank you Lin On 9/22/08, Vitaly Chaban <[EMAIL PROTECTED]> wrote: > > Hi > > how many water molecules used to run MD? > > > > what is the crit

[gmx-users] Atom type: N inside the R-N(CH3)3

Hi What is the atom type of Nitrogen inside the molecule R-N(CH3)3 ? I check the ffG53a5.itp and ffG53a6.itp and the related Gromos FF papers. There are 6 atom types for Nitrogen. N peptide nitrogen (NH) NT terminal nitrogen (NH2) NL terminal nitrogen (NH3) NR aromatic

[gmx-users] Search more information of Atom type: N inside the R-N(CH3)3

Hi What is the atom type of Nitrogen inside the molecule R-N(CH3)3 ? I check the ffG53a5.itp and ffG53a6.itp and the related Gromos FF papers. There are 6 atom types for Nitrogen. N peptide nitrogen (NH) NT terminal nitrogen (NH2) NL terminal nitrogen (NH3) NR aromatic

[gmx-users] #include "ffXXX.itp"

Hi The command #include "ffXXX.itp" is putting in the .top file. I was told that this command will automatically assign the force field parameters which I did not assign in my .top file. I want to print out the complete force field paramters which the command "#include "ffXXX.itp" assigned. Woul

[gmx-users] #include "ffXXX.itp"

HI The command #include "ffXXX.itp" is putting in the .top file. How does this command automatically assign the force field parameters which I did not assign in my .top file? Is it based on the atom types which I assign in my .top file? Then, all the force field parameters from "include ff

[gmx-users] Forming a micelles

Hi I heard that it takes very long to see a micelle forming. How long should be the simulation time to see the micelle forming? How many nanoseconds to put on the simulation? Is there any particular difference to simulate the micelles than other system? My simulation steps are 1. prepare the topo

[gmx-users] Re: #include "ffXXX.itp"

o, [bonds] ; ai aj funct 8 9 gb_28 is correct... [bonds] ; ai aj funct 8 9 is INCORECT... and 8 , 9 will NOT be automatically bonded, right? The same for the nonbonded parts, right? Thank you Lin On 9/22/08, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: &g

[gmx-users] The box size and the # of the solute / water molecules?

Hi What size of the simulation system can be really represent the real situation? Once I decide the box size, the water density can determine the # of water molecules to put in. And, the concentration can determine the # of the solute to put in. Is the procedure correct? Thank you Lin __

[gmx-users] Forming a micelles

Hi Would you please say more about your system? How do you design / decide your simulation size of 100 surfactants +100 co-surfactants + 4000 water molecules?? How many surfactants will form a micelle? How many atoms does one surfactant have? How many atoms does one co-surfactant have? Do you sta

[gmx-users] TIP4P, TIP4P-Ew

Hi Is there TIP4P-Ew in the Gromacs 3.3.3 available? In the top file, there is only tip4p.top and tip4p.gro. Are they the same as TIP4P-Ew model? Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/

[gmx-users] TIP4P, TIP4P-Ew

Hi Is it the only thing that I have to do ? => "get the original paper and adapt the tip4p.top to a tip4p-ew.top" Then, I can say my system is under the water model-TIP4P-Ew. And, other simulation procedures are all the same for any kind of water model. Am I right? Thank you Lin > Hi > Is

[gmx-users] [EMAIL PROTECTED]

Hi How about the tip4p.gro ? Should I modify it? If so, how to modify it? Thank you Lin > Hi > Is there TIP4P-Ew in the Gromacs 3.3.3 available? > > In the top file, there is only tip4p.top and tip4p.gro. > > Are they the same as TIP4P-Ew model? TIP4P-Ew is parameterization of TIP4P for tre

[gmx-users] TIP4P, TIP4P-Ew

Hi There are several parameters to determine a TIP4P or TIP4P-Ew water. r(OH), Å HOH, deg r(OM), Å A × 10−3, kcal Å12/mol B, kcal Å6/mol q(M) q(H) dipole moment . . . etc But, from the tip4p.itp, I only found r(OH), Å HOH, deg q(M) q(H) where are the other parameters to put in? Thank you Li

[gmx-users] TIP4P, TIP4P-Ew

HI I followed the tutorials http://md.chem.rug.nl/education/mdcourse/MDpract.html the procedure is 1. create the box Use a standard cubic box and be sure that the protein does not see its images. This means that the distance from the the box wall should be greater than half of the cut-off (1.4 nm

[gmx-users] TIP4P-Ew.gro

Hi I want to prepare for the TIP4P-Ew.gro. Is TIP4P-Ew.gro exactly equal to TIP4P.gro which is found in the Gromacs file ? Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search

[gmx-users] #define gi_2 ; tetrahedral centres

Hi I found this improper dihedral angle type #define gi_2 35.26439 334.84617 ; tetrahedral centres 80 for -N-(CH3)3- group and in my .top file [dihedrals] ; ai aj ak al funct N CH3CH3 CH32 gi_2 Is this right? Thank you Lin

[gmx-users] The Warning: you should increase table-extension in your mdp file

Hi I put a +1 charge molecule in gas phase and run MD without adding the Counter ions. And, I got the following warning: Although I checked the manual, I don't know how to increase the Table-extension. Thank you Lin Warning: 1-4 interaction between 12 and 19 at distance 1.469 which is larger th

[gmx-users] .pdb to .gro => the atoms are not conneced with VMD

Hi I make .pdb file to .gro file. With the VMD, the atoms are seen NOT conneced. Why? Is there any possible errors in my .gro file? Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search

[gmx-users] MD => system exploding

HI When I run MD, my system is exploding. And, I found after minimisation, the atoms of my molecule are seperated apart. The overall charge of my system is +1, and I put one molecule in the gas phase to do the structure test. But, it was already exploding. Is it hard for a +1 charge molecule to

[gmx-users] .pdb to .gro => the atoms are not conneced with VMD

Hi .pdb to .gro => the atoms are not conneced with VMD >From "Lu Tian"=> When .pdb convert to .gro,connecting information will lost,if the distance between two atoms in .gro is too long,they won't be connected. Can Gromacs recognize that they are connected from the .gro file? Thank you Lin _

[gmx-users] How to assign/make ionion bonds ?

Hi How to assign / make ionion bonds? Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)sub

[gmx-users] The structure property

Hi >From the following tutorial, the protein pdb file is downloaded from the Protein Data Bank. Before running the MD simulation, we have to make sure the structure property. I have some questions about this tutorials. http://nmr.chem.uu.nl/~tsjerk/course/md-tutorial/ 1. Make sure that there are

[gmx-users] The code : from .pdb to .gro

Hi Could anyone please to direct me the code / the command (pdb2gmx) , which can transfer .pdb file to .gro file? Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archi

[gmx-users] H2O water density = 6.4617 g/l << 1000 g/l

Hi I am creating the water box with the following command. The maxsol = 800; but # of SOL = 27; The H2O water density = 6.4617 g/l << 1000 g/l Did I do anything wrong on my genbox command or 1w.gro file? Thank you Lin genbox -cp 1w.gro -cs 1w.gro -o box.gro -box 5 5 5 -maxsol 800 Output con

[gmx-users] Re: H2O water density = 6.4617 g/l << 1000 g/l

HI As Mark described , > "So when you tile these cubes of side length 1.86nm in a 3x3x3 grid, you > over-fill a cube of side length 5nm and get 27 water molecules. Use the > standard water .gro files in the distribution and then minimize and > equilibrate. " And, how could I find the standard wa

[gmx-users] Fatal error, spc.itp", line 41

Hi I have the following error and I could not solve it after checking all the possible solutions on line. Thank you Lin --- Program grompp, VERSION 3.3.3 Source code file: toppush.c, line: 1193 Fatal error: [ file "/usr/local/gromacs/share/gro

[gmx-users] tip3p.gro

Hi In the file , /usr/local/gromacs/share/gromacs/top/ there is a document named tip3p.itp but there is no tip3p.gro how to create the tip3p.gro Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gm

[gmx-users] Fatal error, spc.itp", line 41

Hi I still have no idea about this. Some useful information from Archive is the application on using GROMACS' spc topology with ffamber. But, I am using Gromacs straight without ffamber. How should I solve the problem? Thank you Lin ___ gmx-users maili

[gmx-users] mpi- gromacs

Hi Here is my pdb file. #!/bin/bash #PBS -l nodes=2 cat $PBS_NODEFILE echo Working directory is $PBS_O_WORKDIR cd $PBS_O_WORKDIR mpirun -np 2 g_energy_mpi -f minim_ener.edr -o minim_ener.xvg 11 0 Then, it showed Fatal error: No energy terms selected How to fix the problem Thank you Lin __

[gmx-users] The question from the tutorial: Add water spc216.gro

romacs". Apparently the spc.itp is included in the wrong place in your topology file. Time to read chapter 5 of the manual and get acquainted with the topology file format. Cheers, Tsjerk -- Forwarded message -- From: Chih-Ying Lin <[EMAIL PROTECTED]> Date: Thu, Oct 30,

[gmx-users] WARNING 1 [file aminoacids.dat, line 1]

Hi My system did not include protein. When I run grompp to add water, it showed the warning. WARNING 1 [file aminoacids.dat, line 1] Could I just negect the warning since no protein in my system? Thank you Lin ___ gmx-users mailing listgmx-users@gro

[gmx-users] WARNING 1 [file aminoacids.dat, line 1]

Hi I used the command. grompp -f fullmd.mdp -c minimized_water.gro -p xxx.top -o fullmd.tpr It showed the following WARNING. WARNING 1 [file aminoacids.dat, line 1] My system did not include any protein. So, could I skip/neglect the WARNING?? Thank you Lin The following is the message after s

[gmx-users] The non-protein system => .mdp file ?

Hi There are A_molecules, ion_Br , and water in the system and I will make the .mdp files for the system. In the .mdp file, energygrps, temperature coupling need to indicate the specified groups. Could I just indicate these three kinds of groups, A_molecules, ion_Br, and water ? However, here is

[gmx-users] .gro => atom number

Hi .gro file MD of 2 waters, t= 0.0 6 1ABC OW11 0.126 1.624 1.679 0.1227 -0.0580 0.0434 1ABC HW22 0.190 1.661 1.747 0.8085 0.3191 -0.7791 1ABC HW33 0.177 1.568 1.613 -0.9045 -2.6469 1.3180 2ABC OW14 1.275 0.053 0.622 0.2519 0.3140 -0.

[gmx-users] Sorry

Hi Tsjerk and all Gromacs contributors: I am very sorry about my inappropriate ways of asking questions. I am really totally new in Gromacs, MD, Linux, C programmings, and Bio-tech. No one can discuss with me locally so the thing I can do is to post all my questions on the mailing lists. Before t

[gmx-users] spc.itp:HEAVY_H

Hi In the spc.itp file, Is the HEAVY_H = Deuterium ? Then, H2O become D2O ? Thank you Lin #ifdef _FF_GROMOS96 #ifdef HEAVY_H 1 OW 1SOL OW 1 -0.829.95140 2 H 1SOLHW1 1 0.414.03200 3 H 1SOLHW2

[gmx-users] ions.itp => no BR- ion defined (FF_Gromos 96)

Hi In the ions.itp, there is no BR- ion defined (FF_Gromos 96). But, it was defined in FF_OPLS. How did people solve the problem? Could I simply use all of BR-atom (assign it a -1 charge) non-bonded parameters in FF_Gromos96 instead? Thank you Lin __

[gmx-users] tip3p.itp => OWT3, HW vs. ffG53a6nb.itp => OW, H

Hi Here are part of tip3p.itp and ffG53a6nb.itp. tip3p.itp => OWT3, HW ffG53a6nb.itp => OW, H To make the simulation run, I attempt to replace OWT3 and HW with OW and H in my tip3p.itp file. Does it make sense ? In tip3p.itp, OWT3, HW are not defined in a specific / limited force field ?? Than

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