Hi Chris Thanks very much for your help. The reason I used pull_init1 = 0 is because this is the value that is used in the tutorial. Maybe I am misinterpreting its meaning. In the tutorial it says that you do not have to specify a value separately for each configuration. I am now thinking that in my case this does not apply ? Should I set pull_init to the distance between the molecules at the first configuration?
Many thanks Gavin [email protected] wrote: > Gavin, let's take g_wham out of the picture for now to simplify > things. First, you umbrella is pretty strange. You want them to have a > distance of 0.0 nm (pull_init1 = 0)??? > > So let's look at making a histogram from your raw data. > > 1. cat pullx.xvg |awk '{print sqrt($1,$5*$5+$6*$6+$7*$7)}' > my.dist > 2. ./histo my.dist 0.01 > my.histo > ** select the bin width 0.01 so that the curve is still smooth but > also keep the number small for precision. > ** compile the histo.c code below to get ./histo as follows (gcc > histo.c -o histo -lm) > 3. Make a plot of the histogram and post it on the internet (e.g. > using photobucket website) > 4. reply with a link to your histogram. > > #### PS: i make no claim about the accuracy of the histo.c program so > if you use it for other activities then its at your own risk. In fact, > I think that there are cases where the very fist value is reported > incorrectly, but that should not matter here. > > #include <stdio.h> > #include <stdlib.h> > #include "math.h" > > const int LINE_SIZE=1000; > > void showUsage(const char *c){ > printf("Usage: %s <input_file> <binwidth> [<min> <max>]\n",c); > } > > int main(int argn, char *args[]){ > char linein[LINE_SIZE]; > FILE *f; > int *data; > int nbin,tot,i; > double min,max,bin,c; > > if ((argn!=3 &&argn!=5)|| sscanf(args[2],"%lf",&bin)!=1){ > showUsage(args[0]); > exit(1); > } > > if((f=fopen(args[1],"r"))==NULL){ > printf("Error: unable to open file\n"); > showUsage(args[0]); > exit(1); > } > while(fgets(linein,LINE_SIZE,f)!=NULL){ > if((sscanf(linein,"%lf",&c))!=1)continue; > if(c<min)min=c; > if(c>max)max=c; > } > fclose(f); > > if (argn==5){ > if(sscanf(args[3],"%lf",&min)!=1 || sscanf(args[4],"%lf",&max)!=1){ > showUsage(args[0]); > exit(1); > } > } > > min=floor(min/bin)*bin; > max=ceil(max/bin)*bin; > > nbin=(int)ceil((max-min)/bin); > data=(int *)malloc((nbin+1)*sizeof(int)); > if(data==NULL){ > printf("Memory allocation error\n"); > exit(1); > } > for(i=0; i<=nbin; ++i){ > data[i]=0; > } > > tot=0; > if((f=fopen(args[1],"r"))==NULL){ > printf("Error: unable to open file on second attempt ... > programming error?\n"); > exit(1); > } > while(fgets(linein,LINE_SIZE,f)!=NULL){ > if((sscanf(linein,"%lf",&c))!=1)continue; > ++data[(int)ceil((c-min)/bin)]; > ++tot; > } > fclose(f); > > //Bin 0 only holds the absolute minimum value > i=1; > > printf("%lf\t%lf\n",min+bin*((double)i-0.5),(double)(data[0]+data[1])/(double)tot); > > for(i=2; i<=nbin; ++i){ > > printf("%lf\t%lf\n",min+bin*((double)i-0.5),(double)data[i]/(double)tot); > } > } > > > > -- original message -- > > Hi Guys > > I am having great difficulty generating a histogram of the correct shape > from g_wham. I am running umbrella sampling on one configuration fo two > molecules at a fixed distance using the following > pull parameters. ( I am just running one configuration to begin with so > that can make sure that the shape of my distribution is correct). > > pull = umbrella > pull_geometry = distance > pull_dim = Y Y Y > pull_start = yes > pull_ngroups = 1 > pull_group0 = cage_1 > pull_group1 = cage_2 > pull_init1 = 0 > pull_rate1 = 0.0 > pull_k1 = 2000 > pull_nstxout = 100 > pull_nstfout = 100 > > I have set the force constant quite high in the hope that the system > will sample the equilibrium distance much more often than the distances > accessible form the harmonic potential. In the plot of count vs distance > I get an upside down bell curve in which there is a larger distribution > at the extremeties of the curve. Does anyone know why this may be > happening? If so please let me know. Am I right in assuming that the x > axis in the histo.xvg file is the distance between the centres of masses > of the two molecules? > > Cheers > > Gavin > > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
