Justin,Thank you for your comments after finishing the MD production run for up to 20 ns...
Since this step was over very quickly, now I have a simple question ¿How long, in human time, should a production run last?
The production run was carried out in six processors Intel Xeon (R) E5405 2.00 GHz. The last few lines of the md_0_1.log are:
-----------------------------------------
Parallel run - timing based on wallclock.
NODE (s) Real (s) (%)
Time: 180685.417 180685.417 100.0
2d02h11:25
(Mnbf/s) (GFlops) (ns/day) (hour/ns)
Performance: 232.900 12.351 9.564 2.510
-----------------------------------------
Is this correct? In my opinion it should lasted much more longer...
Before reaching this point, this is an update of what we did...
First we eliminated the SOL_SOL group and the only special index group
was Protein_DMPC.
Since the NVT equilibration failed, we took option # 2 of the "Advanced Troubleshooting", for the 1st phase of Equilibration.
After this step we proceeded with the equilibration phase 2 with a 1-ns NPT equilibration which ended fine.
Next, we proceeded with a 20 ns production run. Thus, the modified lines of the .mpd file found in the tutorial page were:
nsteps = 10000000 ; 2 * 10000000 = 2000 ps (20 ns) tc-grps = Protein DMPC SOL comm-grps = Protein_DMPC SOL With this instructions the 20 ns simulation took 2d02h11:25 I believe the "error" comes from the line constrains = all-bonds which surely must be changed to constrains = none or hbonds Looking forward to your comments... Much obliged, Ramon El 30/03/2011 12:25 p.m., Justin A. Lemkul escribió:
Dr. Ramón Garduño-Juárez wrote:Dear all, Dear Justin,This time I want to ask the gurus about this problem I encountered in the Equilibration step of my system made of 3 individual (small) protein chains in a solvated DMPC bilayer, no ions present since the protein system is neutral...Following the tutorial I started with make_ndx_d -f em_after_solv.gro -o index_after_solv.ndx for which I got the following list: ----------------------------------------------------------------- Reading structure file Going to read 0 old index file(s) Analysing residue names: There are: 129 Protein residues There are: 123 Other residues There are: 3215 Water residues Analysing Protein...Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...0 System : 16649 atoms 1 Protein : 1346 atoms 2 Protein-H : 1025 atoms 3 C-alpha : 129 atoms 4 Backbone : 387 atoms 5 MainChain : 519 atoms 6 MainChain+Cb : 636 atoms 7 MainChain+H : 649 atoms 8 SideChain : 697 atoms 9 SideChain-H : 506 atoms 10 Prot-Masses : 1346 atoms 11 non-Protein : 15303 atoms 12 Other : 5658 atoms 13 DMPC : 5658 atoms 14 Water : 9645 atoms 15 SOL : 9645 atoms 16 non-Water : 7004 atoms -----------------------------------------------------Since I did not add ions I have formed a (merged) group named SOL_SOLWhy would you merge solvent with itself?after chosing 15 | 15 , and another merged group named Protein_DMPC by choosing 1 | 13...Next, I started the NVT equilibration with:grompp_d -f nvt.mdp -c em_after_solv.gro -p topol_mod_lip_solv.top -n index_after_solv.ndx -o nvt.tprThe nvt.mpd file is the same as the one given in the tutorial, the only changes I made were:tc-grps = Protein DMPC SOL_SOL and comm-grps = Protein_DMPC SOL_SOLI would think that using this weird SOL_SOL group would create problems related to degrees of freedom, etc. If you have no ions, there is no need to merge any sort of solvent-related groups.After this I ran mdrun_mpi_d -v -deffnm nvtWhen this process is finished I looked at the resulting nvt.gro file and found the following:1) The 3 protein chains complex is fine, at the center of the box as it should be, but 2) The 2 DMPC layer are separated (splitted) leaving a large gap between them forming a )( shape where the top and bottom of this figure contain one layer of DMPC plus water molecules, while in the narrow section the protein complex is found... In the void between the two DMPC layers no water molecules are present... Very odd!...Please advice...This is covered in the "Advanced Troubleshooting" section of my tutorial:http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/advanced_troubleshooting.html-JustinCheers, Ramon Garduno
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