<html><body><div style="color:#000; background-color:#fff; font-family:arial, helvetica, sans-serif;font-size:12pt"><div><span>Actually, I am confused somehow. <br></span></div><div><span>I want to equilibrate the system. It contains popc and water. To equilibrate it, using .mdp file I use the nvt.mdp file as below.</span></div><div><span><br></span></div><div><span>title = NVT equilibration for POPC<br>define = -DPOSRES ; position restrain the protein<br>; Run parameters<br>integrator = md ; leap-frog integrator<br>nsteps = 50000 ; 2 * 50000 = 100 ps<br>dt = 0.002 ; 2 fs<br>; Output control<br>nstxout =
100 ; save coordinates every 0.2 ps<br>nstvout = 100 ; save velocities every 0.2 ps<br>nstenergy = 100 ; save energies every 0.2 ps<br>nstlog = 100 ; update log file every 0.2 ps<br>; Bond parameters<br>continuation = no ; first dynamics run<br>constraint_algorithm = lincs ; holonomic constraints <br>constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained<br>lincs_iter = 1 ; accuracy of
LINCS<br>lincs_order = 4 ; also related to accuracy<br>; Neighborsearching<br>ns_type = grid ; search neighboring grid cels<br>nstlist = 5 ; 10 fs<br>rlist = 1.2 ; short-range neighborlist cutoff (in nm)<br>rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)<br>rvdw = 1.2 ; short-range van der Waals cutoff (in nm)<br>; Electrostatics<br>coulombtype = PME ; Particle Mesh Ewald for long-range
electrostatics<br>pme_order = 4 ; cubic interpolation<br>fourierspacing = 0.16 ; grid spacing for FFT<br>; Temperature coupling is on<br>tcoupl = V-rescale ; modified Berendsen thermostat<br>tc-grps = POPC SOL ; two coupling groups - more accurate<br>tau_t = 0.1 0.1 ; time constant, in ps<br>ref_t = 323 323 ; reference temperature, one for each group, in K<br>; Pressure coupling is
off<br>pcoupl = no ; no pressure coupling in NVT<br>; Periodic boundary conditions<br>pbc = xyz ; 3-D PBC<br>; Dispersion correction<br>DispCorr = EnerPres ; account for cut-off vdW scheme<br>; Velocity generation<br>gen_vel = yes ; assign velocities from Maxwell distribution<br>gen_temp = 323 ; temperature for Maxwell distribution<br>gen_seed = -1 ; generate a random seed<br><br><br></span></div><div><span><br></span></div><div><span> I enter this command:</span></div><div><span># grompp -f nvt.mdp -c em.gro -p popc.top -o
nvt.tpr</span></div><div><br><span></span></div><div><span>Getting this </span><span>fatal error:<br>Group POPC not found in index file.<br>Group names must match either [moleculetype] names<br>or custom index group names,in which case you<br>must supply an index file to the '-n' option of grompp. <br></span></div><div><br><span></span></div><div><span>I don't </span><span>need </span><span>index file, do I? What is the problem with my .mdp file?</span></div><div><br><span></span></div><div><span>Cheers,</span></div><div><span>Shima<br></span></div><div><br><span></span></div><div><span><br></span></div><div><span><br></span></div><div><br></div> <div style="font-family: arial, helvetica, sans-serif; font-size: 12pt;"> <div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"> <div dir="ltr"> <font size="2" face="Arial"> <hr size="1"> <b><span style="font-weight:bold;">From:</span></b> Justin A. Lemkul
<jalemkul@vt.edu><br> <b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org> <br> <b><span style="font-weight: bold;">Sent:</span></b> Sunday, April 29, 2012 3:10 AM<br> <b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] Make an index file<br> </font> </div> <br>
<br><br>On 4/28/12 2:06 PM, Peter C. Lai wrote:<br>> #2<br>><br>> Generally a good idea to keep the names consistent, however - why are you using<br>> POP in the coordinate file instead of POPC?<br><br>If it is a .pdb file, the standard residue name occupies 3 characters. Many <br>files (including those from Tieleman) are distributed with such names.<br><br>To the OP's original question - the commands you issue depend on what you're <br>trying to achieve. What group do you need to create?<br><br>-Justin<br><br>> --<br>> Sent from my Android phone with K-9 Mail. Please excuse my brevity.<br>><br>> Shima Arasteh <<a ymailto="mailto:shima_arasteh2001@yahoo.com" href="mailto:shima_arasteh2001@yahoo.com">shima_arasteh2001@yahoo.com</a>> wrote:<br>><br>> Dear gmx users,<br>> I want to simulate POPC in water. In equilibration step, I have to make an<br>> index file.
But when I enter this command, I do not know to choose which<br>> group to make a suitable .ndx file which matches the molecule types and<br>> molecules sections in .top file .<br>><br>> The .top file contains these:<br>><br>><br>> [ moleculetype ]<br>> ; Name nrexcl<br>> POPC 3<br>> .<br>> .<br>> .<br>> .<br>> [ system ]<br>> ; name<br>> POPC in water<br>><br>> [ molecules ]<br>> ; name number<br>> POPC 128<br>> SOL 3800<br>><br>><br>> It is the command I enter:<br>> # make_ndx -f em.gro -o index.ndx<br>> 0 System : 18056 atoms<br>> 1 Other : 6656 atoms<br>> 2 POP :
6656 atoms<br>> 3 Water : 11400 atoms<br>> 4 SOL : 11400 atoms<br>> 5 non-Water : 6656 atoms<br>><br>> nr : group ! 'name' nr name 'splitch' nr Enter: list groups<br>> 'a': atom & 'del' nr 'splitres' nr 'l': list residues<br>> 't': atom type | 'keep' nr 'splitat' nr 'h': help<br>> 'r': residue 'res' nr 'chain' char<br>> "name": group 'case': case sensitive 'q': save and quit<br>> 'ri': residue index<br>><br>> Now, what is the correct answer? Anybody can suggest me?<br>><br>> Thanks in advance,<br>> Shima<br>> ge<br>><br>><br>><br><br>-- <br>========================================<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>MILES-IGERT Trainee<br>Department of Biochemistry<br>Virginia
Tech<br>Blacksburg, VA<br>jalemkul[at]<a target="_blank" href="http://vt.edu">vt.edu</a> | (540) 231-9080<br>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br><br>========================================<br>-- <br>gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>http://lists.gromacs.org/mailman/listinfo/gmx-users<br>Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<br><br><br> </div> </div> </div></body></html>