Re: [gmx-users] Concentration of Urea in urea solvation box
Hello All, Thank you very much for your suggestions. I think I have understood it.. Thanks a lot.. :) Regards, Monika On Fri, 5 Sep 2008, Anil Kumar wrote: As Peter has said you have to maintain the ratio of water molecule with respect to urea to get the desired concentration. So, in your case your system must have ratio of Water:Urea = 6.9375:1 (what i understood from the logic of calculation) for 8m Urea concentration (Plz note urea concentration is usually taken in molal not in molar..be careful!) You can start with the default urea+h2o.gro file of gromacs which has concentration of 6m...and do some editing according to your desired concentration followed by density adjustment and equilibrate it for sometime thats it. with regards ___ gmx-users mailing listgmx-users@gromacs.org http://www.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
[gmx-users] Concentration of Urea in urea solvation box
Hi All, This is a trivial question. But I am quite puzzled about it, and I really need someone's kind help. I want to prepare 8M urea solution box, for which I might need to know input as number of water molecules and of urea. Now my query is how to make sure of these exact number of molecules. I know its really a basic question. One thing could be by experiment if we can make sure exact number of moles of water added to make molar solution. But i dont have any access to such wet lab things. So if anyone can help me out how to do these back end calculations. Another query is will the box size also play a role? Please be patient with this trivial query, but this simple calculation question is baffling me from quite a few days. Thanks in advance, Regards, Monika ___ gmx-users mailing listgmx-users@gromacs.org http://www.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
[gmx-users] AFM: .pdo output format
Dear All, I am using pull code to perform AFM on some protein. My pull dimensions are pulldim as Y Y Y for x,y and z coordinates. the output .pdo files are generated, and as far as I have understood, it will get the .pdo output as: time (t), position of ref group (xr,yr,zr), position of pulled group(xp,yp,zp) and position of spring (xs,ys,zs) and accordingly, I am getting 10 columns output: t xr yr zr xp yp zp xs ys zs In the manual it is written that "position of pulled group and spring are in absolute coordinates. Subtract the reference coordinate to get the position relative to the pulled group." which I suppose means that the extension (difference between the pulled group and reference group) should be like = dist=sqrt( (xr-xp)2 + (yr-yp)2 + (zr-zp)2 ) But when I am calculating this way, I am getting very less distance values, which otherwise, when i am doing geometry calculations, they are coming quite higher. I am quite confused. I think I am missing something very important which I am not able to make out. If anyone can please help me out Thanks a lot in advance, Regards, Monika Sharma ___ gmx-users mailing listgmx-users@gromacs.org http://www.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
Re: [gmx-users] Question about Berendsen thermostat and Nose-Hoover temp coupling
Hi Lin! I personally feel increasing the temperature in increments better than giving sudden temperature jump to protein. Regarding temp coupling, both have their limitations. Berendsen is a weak coupling, so can be used for initial runs. Later you can use Nose-Hoover after the proper equilibration is done. However, in case of Nose-Hoover, you might have to select the tau_t carefully, or you will get very large oscillations. PS: Others please do correct me, if I will be thinking a bit wrong somewhere. Cheers! Monika On Mon, 21 Jul 2008, Chih-Ying Lin wrote: Hi My system has been dealt with minimisation and the system was kept constant at 0 K. Then, I want to increate the temperature to 300 K using the Berendsen thermostat. Should I increase the temperature of the system step by step... ? increase temp from 0 K to 50 K 51 K - 100 K 101 K - 150 K 151 K - 200 K 201 K - 250 K 251 K - 300 K seperately? or increase temp from 0 K to 300 K at one time? After the temperature of the system reaches 300 K, should I use Nose-Hoover temperature coupling to keep the system at the equliibration on 300 K? I have read manual though. Thanks a lot Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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
Re: [gmx-users] Simulated Annealing problem
On Sat, 22 Mar 2008, Mark Abraham wrote: Hello, Thanks for reply. I am sorry for typo here, but just checked the .mdp file. Its correct in the input file. In the log file, it says for annealing as: grpopts: nrdf: 8093.62 55326.4 ref_t:300 300 tau_t:0.1 0.1 anneal: Single Single ann_npoints: 7 7 ann. times [0]: 0.0 250.0 250.0 250.0 250.0 500.0 1000.0 ann. temps [0]:300.0 330.0 360.0 345.0 330.0 315.0 300.0 ann. times [1]: 0.0 250.0 250.0 250.0 250.0 500.0 1000.0 ann. temps [1]:300.0 330.0 360.0 345.0 330.0 315.0 300.0 By consistency, is it means equal intervals of time? Regards, Monika [EMAIL PROTECTED] wrote: Dear All, I am trying to do simulated annealing for solvated protein system. the excerpts of the file is as: energygrps = protein non-protein ;Temperature coupling tcoupl = Berendsen tc-grps = protein non-protein tau_t= 0.1 0.1 ref_t= 300 300 ;Pressure coupling Pcoupl = berendsen Pcoupltype = isotropic tau_p= 1.0 compressibility = 4.5e-5 ref_p= 1.0 ;Velocity generation gen_vel = yes gen_temp = 300 gen_seed = 173529 ; SIMULATED ANNEALING ; Type of annealing for each temperature group (no/single/periodic) annealing= single single ; Number of time points to use for specifying annealing in each group annealing_npoints= 7 7 ; List of times at the annealing points for each group annealing_time = 0 250 250 250 250 500 500 1000 0 250 250 250 250 500 1000 ; Temp. at each annealing point, for each group. annealing_temp = 300 330 360 345 330 315 300 300 330 360 345 330 315 300 The log however shows that the ref_t increase from 300K to 330K in 250ps and then it decreases to 300K in 750ps, and the temperature is aftwerwards maintained at 300K. From the input, it should increase to 360K and then decrease to 345,330,315 and 300K. But this is not happening. Read manual section 7.3.15 - the number of annealing_time entries is not consistent. To check whether its because of temperature couple, t_coupling was removed. But then during .tpr formation, it complained of providing two groups. Why haven't you copied and pasted the actual error message? This approach shouldn't work, as you would have expected if you'd read section 3.7 of the manual. Will then SA wont take two groups (protein and non-protein)? Why is it so then the temperature rises till 330 only, not after that, and it comes down? grompp should be describing the annealing profile it's doing. What did it say? Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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
Re: [gmx-users] Simulated Annealing problem
Hello, Thanks for reply. I am sorry for typo here, but just checked the .mdp file. Its correct in the input file. In the log file, it says for annealing as: grpopts: nrdf: 8093.62 55326.4 ref_t:300 300 tau_t:0.1 0.1 anneal: Single Single ann_npoints: 7 7 ann. times [0]: 0.0 250.0 250.0 250.0 250.0 500.0 1000.0 ann. temps [0]:300.0 330.0 360.0 345.0 330.0 315.0 300.0 ann. times [1]: 0.0 250.0 250.0 250.0 250.0 500.0 1000.0 ann. temps [1]:300.0 330.0 360.0 345.0 330.0 315.0 300.0 By consistency, is it means equal intervals of time? Regards, Monika [EMAIL PROTECTED] wrote: Dear All, I am trying to do simulated annealing for solvated protein system. the excerpts of the file is as: energygrps = protein non-protein ;Temperature coupling tcoupl = Berendsen tc-grps = protein non-protein tau_t= 0.1 0.1 ref_t= 300 300 ;Pressure coupling Pcoupl = berendsen Pcoupltype = isotropic tau_p= 1.0 compressibility = 4.5e-5 ref_p= 1.0 ;Velocity generation gen_vel = yes gen_temp = 300 gen_seed = 173529 ; SIMULATED ANNEALING ; Type of annealing for each temperature group (no/single/periodic) annealing= single single ; Number of time points to use for specifying annealing in each group annealing_npoints= 7 7 ; List of times at the annealing points for each group annealing_time = 0 250 250 250 250 500 500 1000 0 250 250 250 250 500 1000 ; Temp. at each annealing point, for each group. annealing_temp = 300 330 360 345 330 315 300 300 330 360 345 330 315 300 The log however shows that the ref_t increase from 300K to 330K in 250ps and then it decreases to 300K in 750ps, and the temperature is aftwerwards maintained at 300K. From the input, it should increase to 360K and then decrease to 345,330,315 and 300K. But this is not happening. Read manual section 7.3.15 - the number of annealing_time entries is not consistent. To check whether its because of temperature couple, t_coupling was removed. But then during .tpr formation, it complained of providing two groups. Why haven't you copied and pasted the actual error message? This approach shouldn't work, as you would have expected if you'd read section 3.7 of the manual. Will then SA wont take two groups (protein and non-protein)? Why is it so then the temperature rises till 330 only, not after that, and it comes down? grompp should be describing the annealing profile it's doing. What did it say? Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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
[gmx-users] Simulated Annealing problem
Dear All, I am trying to do simulated annealing for solvated protein system. the excerpts of the file is as: energygrps = protein non-protein ;Temperature coupling tcoupl = Berendsen tc-grps = protein non-protein tau_t= 0.1 0.1 ref_t= 300 300 ;Pressure coupling Pcoupl = berendsen Pcoupltype = isotropic tau_p= 1.0 compressibility = 4.5e-5 ref_p= 1.0 ;Velocity generation gen_vel = yes gen_temp = 300 gen_seed = 173529 ; SIMULATED ANNEALING ; Type of annealing for each temperature group (no/single/periodic) annealing= single single ; Number of time points to use for specifying annealing in each group annealing_npoints= 7 7 ; List of times at the annealing points for each group annealing_time = 0 250 250 250 250 500 500 1000 0 250 250 250 250 500 1000 ; Temp. at each annealing point, for each group. annealing_temp = 300 330 360 345 330 315 300 300 330 360 345 330 315 300 The log however shows that the ref_t increase from 300K to 330K in 250ps and then it decreases to 300K in 750ps, and the temperature is aftwerwards maintained at 300K. From the input, it should increase to 360K and then decrease to 345,330,315 and 300K. But this is not happening. To check whether its because of temperature couple, t_coupling was removed. But then during .tpr formation, it complained of providing two groups. Will then SA wont take two groups (protein and non-protein)? Why is it so then the temperature rises till 330 only, not after that, and it comes down? All suggestions are welcome. Thanking in advance, Regards, Monika ___ gmx-users mailing listgmx-users@gromacs.org http://www.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
Re: [gmx-users] Data generated by g_sas
Hello All, For reference, the output files are as: # This file was created Thu Jan 31 17:27:21 2008 # by the following command: # g_sas -f pro-total-21ns-300K-PT.xtc -s pro-3ns-300K-PT.tpr -o pro-21ns-300K-g_sas-area.xvg -or pro-21ns-300K-g_sas-resarea.xvg -oa pro-21ns-300K-g_sas-atomarea.xvg -q pro-21ns-300K-g_sas-connelly.xvg # # g_sas is part of G R O M A C S: # # Gromacs Runs One Microsecond At Cannonball Speeds # @title "Area per residue" @xaxis label "Residue" @yaxis label "Area (nm\S2\N)" @TYPE xy 10.867478 0.178453 2 1.05816 0.248229 3 1.12171 0.280894 4 1.54811 0.212061 50.532166 0.119596 6 2.05678 0.271594 7 1.433240.18675 8 0.9919 0.156349 90.745497 0.277242 100.193999 0.0824625 110.573983 0.238295 120.934204 0.0959199 130.671052 0.143626 14 0.15924 0.0966806 15 1.143980.19238 16 1.32751 0.240461 170.594131 0.169421 180.256019 0.150048 19 1.24637 0.251035 20 1.186730.13117 210.734073 0.147444 22 1.22901 0.169386 23 0.30032 0.137402 24 1.17923 0.222947 25 0.524570.18227 260.564586 0.198732 This is an excerpt from the output file for g_sas area calculation per residue. Thanking you, Regards, Monika On Thu, 6 Mar 2008, Mark Abraham wrote: [EMAIL PROTECTED] wrote: Hello All, This might sound a bit stupid question. But I have no idea about it. So here I am asking it. I am using g_sas to calculate the solvent accessible area. But I am not able to understand the values the program is giving out. I am using options -or and -oa to get it plotted per residue and atom. It generates three columns data per residue-type and atom-type output. First column for Residue# or atom#. I am confused what the second and third columns corresponds to? If anyone can suggest me. There are no legends provided in the xvgr file generated either. Providing a sample of parts of the output files would be a useful thing to do. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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
[gmx-users] Data generated by g_sas
Hello All, This might sound a bit stupid question. But I have no idea about it. So here I am asking it. I am using g_sas to calculate the solvent accessible area. But I am not able to understand the values the program is giving out. I am using options -or and -oa to get it plotted per residue and atom. It generates three columns data per residue-type and atom-type output. First column for Residue# or atom#. I am confused what the second and third columns corresponds to? If anyone can suggest me. There are no legends provided in the xvgr file generated either. Thanking you, Regards, Monika ___ gmx-users mailing listgmx-users@gromacs.org http://www.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
Re: [gmx-users] unfolding a protein
On Wed, 20 Feb 2008, Siavoush Dastmalchi wrote: Hii!! The time scale you have chosen is very less to see unfolding in proteins of moderate length, because in such a short time u might be able to see just local disturbances only, even at temperature of 400K. You need to increase the production run time, atleast go for 3n. And you might not need constrains of all-bonds to put. Cheers, Monika Hi there, I want to unfold a protein (hen egg white lysozyme) which has got 4 disulfide bounds. I have tried 1 ns of MD at 400 K either in vacuum or hydrated form and it didn't unfold. I know it may need longer time, but it doesn't show any sign of even starting to unfold. I think I am restraining the protein in some way. Please see below the content of ~.mdp file that I use. Would you please let me know how I could unfold a protein using an MD simulation? Do you think unfolding a water soluble protein in vacuum would be faster? Cheers, Siavoush cpp = /lib/cpp include = -I../top integrator = md dt = 0.002 nsteps = 50 nstxout = 1000 nstvout = 1000 nstlog = 100 nstenergy= 100 nstxtcout= 100 xtc_grps = protein sol energygrps = protein sol nstlist = 10 ns_type = grid rlist= 0.8 coulombtype = cut-off rcoulomb = 1.4 rvdw = 1.4 pbc = xyz tcoupl = berendsen tc-grps = protein sol tau_t= 0.1 0.1 ref_t= 400 400 Pcoupl = berendsen Pcoupltype = isotropic tau_p= 1.0 compressibility = 4.5e-5 ref_p= 1.0 gen_vel = yes gen_temp = 400 gen_seed = 173529 constraints = all-bonds ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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
