<font class="Apple-style-span" face="'courier new', monospace">Hi there,</font><div><font class="Apple-style-span" face="'courier new', monospace"><br></font></div><div><font class="Apple-style-span" face="'courier new', monospace">I have a very simple case of a tri alanine (AAA). You can use tleap to create such peptide and save the pdb and amber's parameters.</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace"><br></font></div><div><font class="Apple-style-span" face="'courier new', monospace">Then I do a single point calculation to get the potential energy. I am using mdin like:</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace"><br></font></div><div><div><font class="Apple-style-span" face="'courier new', monospace">cat << EOF >| mdin</font></div><div><font class="Apple-style-span" face="'courier new', monospace">Single point</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace">&cntrl</font></div><div><font class="Apple-style-span" face="'courier new', monospace">imin=0, maxcyc=0,</font></div><div><font class="Apple-style-span" face="'courier new', monospace">ntmin=2,</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace">ntb=0,</font></div><div><font class="Apple-style-span" face="'courier new', monospace">igb=0,</font></div><div><font class="Apple-style-span" face="'courier new', monospace">cut=999,</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace">/</font></div><div><font class="Apple-style-span" face="'courier new', monospace">EOF</font></div></div><div><font class="Apple-style-span" face="'courier new', monospace"><br>
</font></div><div><font class="Apple-style-span" face="'courier new', monospace">Then I test the same input parameters with Namd2, using namd.conf:</font></div><div><font class="Apple-style-span" face="'courier new', monospace"><br>
</font></div><div><div><font class="Apple-style-span" face="'courier new', monospace">cat << EOF >| AAAamb_namd.conf</font></div><div><font class="Apple-style-span" face="'courier new', monospace">outputEnergies 1 # Energy output frequency</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace">DCDfreq 1 # Trajectory file frequency</font></div><div><font class="Apple-style-span" face="'courier new', monospace">timestep 2 # in unit of fs</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace">temperature 300 # Initial temp for velocity assignment</font></div><div><font class="Apple-style-span" face="'courier new', monospace">cutoff 999</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace">switching off # Turn off the switching functions</font></div><div><font class="Apple-style-span" face="'courier new', monospace">PME off # Use PME for electrostatic calculation</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace">amber on # Specify this is AMBER force field</font></div><div><font class="Apple-style-span" face="'courier new', monospace">parmfile AAAamb.prmtop # Input PARM file</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace">ambercoor AAAamb.inpcrd # Input coordinate file</font></div><div><font class="Apple-style-span" face="'courier new', monospace">outputname AAAamb # Prefix of output files</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace">exclude scaled1-4</font></div><div><font class="Apple-style-span" face="'courier new', monospace">1-4scaling 0.833333 # =1/1.2, default is 1.0</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace">minimize 0</font></div><div><font class="Apple-style-span" face="'courier new', monospace">EOF</font></div></div><div><font class="Apple-style-span" face="'courier new', monospace"><br>
</font></div><div><font class="Apple-style-span" face="'courier new', monospace">I have only a 0.001 kcal/mol absolute diff (or relative 0.0037%) for the Elec term, everything else is absolutely the same.</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace"><br></font></div><div><font class="Apple-style-span" face="'courier new', monospace">Then comes gromacs. I convert my prmtop and inpcrd to gromcs top and gro with either acpype or amb2gmx and then doing a single point with file:</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace"><br></font></div><div><div><font class="Apple-style-span" face="'courier new', monospace">cat << EOF >| SPE.mdp</font></div><div>
<font class="Apple-style-span" face="'courier new', monospace">integrator = md</font></div><div><font class="Apple-style-span" face="'courier new', monospace">nsteps = 0</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace">dt = 0.001</font></div><div><font class="Apple-style-span" face="'courier new', monospace">constraints = none</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace">emtol = 10.0</font></div><div><font class="Apple-style-span" face="'courier new', monospace">emstep = 0.01</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace">nstcomm = 1</font></div><div><font class="Apple-style-span" face="'courier new', monospace">ns_type = simple</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace">nstlist = 0</font></div><div><font class="Apple-style-span" face="'courier new', monospace">rlist = 0</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace">rcoulomb = 0</font></div><div><font class="Apple-style-span" face="'courier new', monospace">rvdw = 0</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace">Tcoupl = no</font></div><div><font class="Apple-style-span" face="'courier new', monospace">Pcoupl = no</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace">gen_vel = no</font></div><div><font class="Apple-style-span" face="'courier new', monospace">nstxout = 1</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace">pbc = no</font></div><div><font class="Apple-style-span" face="'courier new', monospace">nstlog = 1</font></div><div>
<font class="Apple-style-span" face="'courier new', monospace">nstenergy = 1</font></div><div><font class="Apple-style-span" face="'courier new', monospace">nstvout = 1</font></div><div><font class="Apple-style-span" face="'courier new', monospace">nstfout = 1</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace">nstxtcout = 1</font></div><div><font class="Apple-style-span" face="'courier new', monospace">comm_mode = ANGULAR</font></div><div><font class="Apple-style-span" face="'courier new', monospace">EOF</font></div>
</div><div><font class="Apple-style-span" face="'courier new', monospace"><br></font></div><div><font class="Apple-style-span" face="'courier new', monospace">Converting gromacs energies (kJ/mol) by dividing the terms by 4.184 and they don't match amber/namd results. See relative diffs (abs(g-a)/max(abs(a),abs(g))):</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace"><br></font></div><div><font class="Apple-style-span" face="'courier new', monospace">Bond: 5.87%</font></div><div><font class="Apple-style-span" face="'courier new', monospace">Angle: 3.49%</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace">Dihe: 0.14%</font></div><div><font class="Apple-style-span" face="'courier new', monospace">vdW: 0.52%</font></div><div><font class="Apple-style-span" face="'courier new', monospace">Elec: 0.17%</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace">Pot.Tot: 5.90%</font></div><div><font class="Apple-style-span" face="'courier new', monospace"><br></font></div><div><font class="Apple-style-span" face="'courier new', monospace">I am very surprised to find this difference, in special for Bond since it's for this term essentially the same equation and parameters. Any ideas of what could be missing here?</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace"><br></font></div><div><font class="Apple-style-span" face="'courier new', monospace">Many thanks,</font></div><div><font class="Apple-style-span" face="'courier new', monospace"><br>
</font></div><div><font class="Apple-style-span" face="'courier new', monospace">Alan</font></div><div><font class="Apple-style-span" face="'courier new', monospace"><br></font></div><div><font class="Apple-style-span" face="'courier new', monospace">-- <br>
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate<br>Department of Biochemistry, University of Cambridge. <br>80 Tennis Court Road, Cambridge CB2 1GA, UK.<br>>><a href="http://www.bio.cam.ac.uk/~awd28">http://www.bio.cam.ac.uk/~awd28</a><<</font><br>
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