<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><DIV>Dear GMX users,</DIV>
<DIV> Recently, I want to caculate the free energy for K+----->NA+ in bulk with GMX4.5.4 using charmm 27 force field. I change ion.itp</DIV>
<DIV>[ moleculetype ]<BR>; molname nrexcl<BR>K 1</DIV>
<DIV>[ atoms ]<BR>; id at type res nr residu name at name cg nr charge </DIV>
<DIV>1 POT 1 K K 1 1 </DIV>
<DIV> </DIV>
<DIV>to</DIV>
<DIV> </DIV>
<DIV>[ moleculetype ]<BR>; molname nrexcl<BR>K 1</DIV>
<DIV>[ atoms ]<BR>; id at type res nr residu name at name cg nr charge mass typeB chargeB massB<BR>1 POT 1 K K 1 1 39.102000 SOD 1 22.989770 </DIV>
<DIV>#ifdef POSRES_K<BR>[ position_restraints ]<BR>; i funct fcx fcy fcz<BR> 1 1 1000000 1000000 1000000<BR>#endif</DIV>
<DIV> </DIV>
<DIV>and include it into .top file.</DIV>
<DIV> </DIV>
<DIV>And I set .mdp file</DIV>
<DIV>; Free energy control stuff<BR>free-energy = yes<BR>init-lambda = 0.0<BR>delta-lambda = 0<BR>foreign_lambda = 0.05<BR>sc-alpha = 0.5<BR>sc-power = 1.0<BR>sc-sigma = 0.3<BR>nstdhdl = 10<BR>separate-dhdl-file =
yes<BR>dhdl-derivatives = yes<BR>dh_hist_size = 0<BR>dh_hist_spacing = 0.1<BR>couple-moltype = K<BR>couple-lambda0 = vdw-q<BR>couple-lambda1 = vdw-q<BR>couple-intramol = no</DIV>
<DIV> </DIV>
<DIV>however when I do EM, there are two warnings and stop.</DIV>
<DIV>WARNING 1 [file min.mdp, line 329]:<BR> The lambda=0 and lambda=1 states for coupling are identical</DIV>
<DIV>Generated 28 of the 28 non-bonded parameter combinations<BR>Generating 1-4 interactions: fudge = 1<BR>Generated 28 of the 28 1-4 parameter combinations</DIV>
<DIV>WARNING 2 [file ion.itp, line 22]:<BR> Some parameters for bonded interaction involving perturbed atoms are<BR> specified explicitly in state A, but not B - copying A to B</DIV>
<DIV>Excluding 3 bonded neighbours molecule type 'gra'<BR>Excluding 2 bonded neighbours molecule type 'SOL'<BR>Excluding 1 bonded neighbours molecule type 'K'<BR>Coupling 1 copies of molecule type 'K'</DIV>
<DIV>NOTE 1 [file topol.top, line 16]:<BR> System has non-zero total charge: 1.000000e+00<BR> </DIV>
<DIV><BR>Analysing residue names:<BR>There are: 1 Other residues<BR>There are: 531 Water residues<BR>There are: 1 Ion residues<BR>Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...<BR>Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...<BR>Number of degrees of freedom in T-Coupling group rest is 3660.00<BR>Largest charge group radii for Van der Waals: 0.040, 0.040 nm<BR>Largest charge group radii for Coulomb: 0.079, 0.079 nm<BR>Calculating fourier grid dimensions for X Y Z<BR>Using a fourier grid of 20x20x30, spacing 0.115 0.115 0.115<BR>Estimate for the relative computational load of the PME mesh part: 0.36<BR>This run will generate roughly 22 Mb of data</DIV>
<DIV>There was 1 note</DIV>
<DIV>There were 2 warnings</DIV>
<DIV>-------------------------------------------------------<BR>Program grompp, VERSION 4.5.4<BR>Source code file: grompp.c, line: 1582</DIV>
<DIV>Fatal error:<BR>Too many warnings (2), grompp terminated.<BR>If you are sure all warnings are harmless, use the -maxwarn option.<BR>For more information and tips for troubleshooting, please check the GROMACS<BR>website at <A href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</A><BR>-------------------------------------------------------</DIV>
<DIV>"Your Proposal is Accepted" (Men In Black)</DIV>
<DIV> </DIV>
<DIV>It seems that </DIV>
<DIV>[ moleculetype ]<BR>; molname nrexcl<BR>K 1</DIV>
<DIV>[ atoms ]<BR>; id at type res nr residu name at name cg nr charge mass typeB chargeB massB<BR>1 POT 1 K K 1 1 39.102000 SOD 1 22.989770 </DIV>
<DIV>do not take effect.</DIV>
<DIV> </DIV>
<DIV>Thanks in advance!</DIV>
<DIV> </DIV>
<DIV>Zhongjin He</DIV></td></tr></table>