[gmx-users] solvate using genbox results in water in the centerofthe bilayer. How to edit pdb file contents in gromacs ?
Dear Chris, Thanks a lot your suggestions. I have started the MD based on your suggestions. I will tell you as soon I will get the results. ok, great. PS: Is this is already reported that Gromacs have some problem with ZERO? No. And I don't believe that gromacs has a problem here. But it is something that you could test. For example... is the z changing at all in your simulation? I only mentioned anything about it because I have no personal knowledge that it works correctly with zeroes from my own experience. That of course doesn't make it incorrect :) but I would prefer for you to try using some set of conditions that I do know personally to work correctly. Regards, Alok ___ 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] solvate using genbox results in water in the >centerofthe bilayer. How to edit pdb file contents in gromacs ?
Dear Chris, Thanks a lot your suggestions. I have started the MD based on your suggestions. I will tell you as soon I will get the results. PS: Is this is already reported that Gromacs have some problem with ZERO? Regards, Alok - Original Message - From: <[EMAIL PROTECTED]> To: Sent: Thursday, October 25, 2007 1:47 PM Subject: [gmx-users] solvate using genbox results in water in the >centerofthe bilayer. How to edit pdb file contents in gromacs ? Dear Chris, Thanks for your time and suggestion. I tried all the possible pressure couplings (including semiisotropic) and run it for around 500ps.Gap between head group and water molecule disappear, but I was getting uneven distribution of water molecules. I am pasting my previous mail again. Hope I will get any solution for my problem. Best Regards, Alok ## Dear Mark, Thanks a lot for your valuable time, and sorry for inappropriate description, I am describing again, I hope thin time I can make it clear. I took preequilibrated POPE.pdb files which already have SPC water molecules I had deleted these water molecules and change the box size at 'Z Axis' only, so I can accommodate more water, then using genbox I had added TIP4P water molecules, but it also added the water molecules in the interior of the bilayer. So I deleted these water by the criteria if the 'Z' coordinate of the water in between the 'Z_min' and 'Z_max' of 'C13' (where branching of the POPE molecules start) atom. After that I got the files which don't have any water at the interior of the bilayer but there is a vaccuum between lipid head group and TIP4P water molecules (I defined it as a ZONE in my previous mail). As discussed in the mailing list so many times I can do same thing by increasing the VdW radius of lipid atoms. But after that I was expecting these vacuum will be vanished and water molecules will spread homogenously after sort span of MD, as suggested in the mailing list. But here problem has started I run MD till 500ps, but water molecules are clustered at some places, at some places there is no water or very less water. i.e. I am getting uneven distribution of water molecules over lipid head groups. So I thought this problem might be due to pressure coupling or type of ensemble I am using (might be I am wrong here !). I ran four different sort MD by using isotropic, semiisotropic, anisotropic pressure coupling and last one no pressure coupling (NVT ensemble). But in all the cases I am getting similar structure at last which is uneven distribution of TIP4P water molecules over head groups. The parameters I used for diffrent couplings all mentioned below. Isotropic: (First Simulation) diffrent = Berendsen Pcoupltype= isotropic tau_p = 2.0 compressibility = 4.5e-5 ref_p = 1 semiisotroic: (Second Simulation) Pcoupl = Berendsen Pcoupltype = semiisotropic tau_p= 2 2 compressibility=0 4.5e-5 ref_p = 0 1.0 What's going on here? Apparently x/y stays the same and Z can scale? I am relatively sure that this is your problem. try this: semiisotroic: (Second Simulation) Pcoupl = Berendsen Pcoupltype = semiisotropic tau_p= 2 2 compressibility = 4.5e-54.5e-5 ref_p= 1.0 1.0 **Note that I personally use tau_p=4 but 2 should be fine also. Also note that there may _possibly_ be some issue with gromacs that makes the zeroes not work as they should, but I would rather suspect that everything is working as it should and that it is just not working as you might expect. Try the above suggestion and let me know hoe it works out. Chris. anisotropic: (Third Simulation) Pcoupl = Berendsen pcoupltype = anisotropic tau_p= 10.0 10.010.0 0 0 compressibility= 4.5e-5 4.5e-5 4.5e-500 0 ref_p = 1.0 1.0 1.0 0 0 0 I would avoid anisotropic. In any event, still I would avoid zeroes. NVT (Fourth Simulation). I hope I make my problem clear.could some one give some idea what parameters/ensemble I should take to overcome this problem. please suggest me where I am doing mistake. Thanks Regards, Alok - Original Message - From: "Mark Abraham" <[EMAIL PROTECTED]> To: "Discussion list for GROMACS users" Sent: Friday, October 19, 2007 11:58 AM Subject: Re: [gmx-users] uneven distribution of water across the bilayer Alok wrote: Dear All, I am trying to simulate lipid-water system (340 POPE
[gmx-users] solvate using genbox results in water in the > centerofthe bilayer. How to edit pdb file contents in gromacs ?
50 to250 ps) using different pressure coupling but still I am not getting the structure which have homogeneous arrangement of water over lipid head group. There is uneven distribution of water across the bilayer. Are these last two observations related, or not? During this sort simulations position restrain on lipid was applied. Check your waters aren't restrained too. I tried Isotropic, semiisotropic,anisotropic pressure coupling with the following parameter, but no luck I think you need to read section 7.3.14 of the manual. You're using combinations of parameter values that don't make sense. Isotropic: Pcoupl = Berendsen Pcoupltype= isotropic tau_p = 2.0 compressibility = 4.5e-5 ref_p = 1 semiisotropic: Pcoupl = Berendsen Pcoupltype = semiisotropic tau_p= 2 2 compressibility= 0 4.5e-5 ref_p = 0 1.0 anisotropic: Pcoupl = Berendsen pcoupltype = anisotropic tau_p= 10.0 10.010.0 0 0 compressibility= 4.5e-5 4.5e-54.5e-50 0 0 ref_p = 1.0 1.0 1.0 0 0 I also tried NVT Ensemble but no success till now. So the problem is something other than the way you're setting up your ensemble. could some one give some idea what parameters I should take to overcome this problem. I searched the mailing list this problem discussed so many time suggestion was after sort simulation (10-20 ps) water will arrange properly,but I am not able to get proper arrangement of water molecules. please suggest me where I am doing mistake. Other parameters od the MDP file. define = -DPOSRES_LIPID integrator = md dt= 0.002 nsteps = 25000 nstcomm = 1 nstxout = 1000 nstvout = 500 nstlog = 100 nstenergy = 100 nstxtcout= 500 xtc_precision= 1000 xtc_grps = POPE SOL energygrps = POPE SOL nstlist = 10 ns_type = grid pbc = xyz rlist = 0.9 coulombtype = PME rcoulomb = 0.9 rvdw = 1.2 fourierspacing = 0.12 pme_order = 6 ewald_rtol = 1e-5 optimize_fft = yes vdw-type = Cut-off gen_vel = yes gen_temp = 300 gen_seed = 173529 constraints = all-bonds constraint_algorithm= lincs unconstrained_start = no lincs_order = 4 lincs_iter = 1 lincs_warnangle = 30 That looks OK at a glance. Mark - Original Message ----- From: <[EMAIL PROTECTED]> To: Sent: Thursday, October 25, 2007 10:37 AM Subject: [gmx-users] solvate using genbox results in water in the centerofthe bilayer. How to edit pdb file contents in gromacs ? You can do it by two different methods. 1) You can increase the default VdW radii of the lipid atoms in /usr/local/ gromacs/share/top/vdwradii.dat file (path might be different from your system), say 0.5 for carbon, so genbox will not add the water inside the bilayer. Cleaner method is to: cp /usr/local/gromacs/share/top/vdwradii.dat ./vdwradii.dat and then modify the local file. but you will find a gap between lipid head groups and water molecules which can be resolved after some ps dynamics. (I personally have not yet got the success ;-) ) Do I understand you to say that for you the gap does not completely dissapear in <500ps? Did you use semiisotropic coupling? Otherwise it will be more difficult for this space to fill in. It should fill in really quite quickly (<<500ps)... has for me. 2) You can write a small script which can delete these water molecules, I wrote a script for the same if you need contact me offline. I have previously posted such a script. It takes 10-30 minutes to run since it's not sophisticated, but it does work very well. http://www.gromacs.org/pipermail/gmx-users/2006-May/021526.html I forgot to mention that in the previously referenced script there is an assumption that you use a 3 atom water molecule. If you use tip4p then you would want if [ "$count" = 3 ]; then count=0 fi to be changed to: if [ "$count" = 4 ]; then count=0 fi and etc for tip5p. Hope it will help Alok - Original Message - Hi I am using editconf to try to add water layers on either side of my bilayer. I use the following command: genbox -cp popc.gro
Re: [gmx-users] solvate using genbox results in water in the centerofthe bilayer. How to edit pdb file contents in gromacs ?
Alok wrote: Dear Chris, Thanks for your time and suggestion. I tried all the possible pressure couplings (including semiisotropic) and run it for around 500ps.Gap between head group and water molecule disappear, but I was getting uneven distribution of water molecules. I am pasting my previous mail again. Hope I will get any solution for my problem. Best Regards, Alok ## Dear Mark, Thanks a lot for your valuable time, and sorry for inappropriate description, I am describing again, I hope thin time I can make it clear. I took preequilibrated POPE.pdb files which already have SPC water molecules I had deleted these water molecules Why not leave them? and change the box size at 'Z Axis' only, so I can accommodate more water, then using genbox I had added TIP4P water molecules, but it also added the water molecules in the interior of the bilayer. So I deleted these water by the criteria if the 'Z' coordinate of the water in between the 'Z_min' and 'Z_max' of 'C13' (where branching of the POPE molecules start) atom. After that I got the files which don't have any water at the interior of the bilayer but there is a vaccuum between lipid head group and TIP4P water molecules (I defined it as a ZONE in my previous mail). The Z-coordinate-based water-removal procedure you describe can't create such a vacuum, so I can't follow your description. As discussed in the mailing list so many times I can do same thing by increasing the VdW radius of lipid atoms. But after that I was expecting these vacuum will be vanished and water molecules will spread homogenously after sort span of MD, as suggested in the mailing list. But here problem has started I run MD till 500ps, but water molecules are clustered at some places, at some places there is no water or very less water. i.e. I am getting uneven distribution of water molecules over lipid head groups. I'm afraid I can't understand what you mean by "uneven distribution" in the absence of a picture or a structure. So I thought this problem might be due to pressure coupling or type of ensemble I am using (might be I am wrong here !). I ran four different sort MD by using isotropic, semiisotropic, anisotropic pressure coupling and last one no pressure coupling (NVT ensemble). But in all the cases I am getting similar structure at last which is uneven distribution of TIP4P water molecules over head groups. I made suggestions about your parameters last time. You don't seem to have followed them. 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
Re: [gmx-users] solvate using genbox results in water in the centerofthe bilayer. How to edit pdb file contents in gromacs ?
= 1 semiisotropic: Pcoupl = Berendsen Pcoupltype = semiisotropic tau_p= 2 2 compressibility= 0 4.5e-5 ref_p = 0 1.0 anisotropic: Pcoupl = Berendsen pcoupltype = anisotropic tau_p= 10.0 10.010.0 0 0 0 compressibility= 4.5e-5 4.5e-54.5e-50 0 0 ref_p = 1.0 1.0 1.0 0 0 0 I also tried NVT Ensemble but no success till now. So the problem is something other than the way you're setting up your ensemble. could some one give some idea what parameters I should take to overcome this problem. I searched the mailing list this problem discussed so many time suggestion was after sort simulation (10-20 ps) water will arrange properly,but I am not able to get proper arrangement of water molecules. please suggest me where I am doing mistake. Other parameters od the MDP file. define = -DPOSRES_LIPID integrator = md dt= 0.002 nsteps = 25000 nstcomm = 1 nstxout = 1000 nstvout = 500 nstlog = 100 nstenergy = 100 nstxtcout= 500 xtc_precision= 1000 xtc_grps = POPE SOL energygrps = POPE SOL nstlist = 10 ns_type = grid pbc = xyz rlist = 0.9 coulombtype = PME rcoulomb = 0.9 rvdw = 1.2 fourierspacing = 0.12 pme_order = 6 ewald_rtol = 1e-5 optimize_fft = yes vdw-type = Cut-off gen_vel = yes gen_temp = 300 gen_seed = 173529 constraints = all-bonds constraint_algorithm= lincs unconstrained_start = no lincs_order = 4 lincs_iter = 1 lincs_warnangle = 30 That looks OK at a glance. Mark - Original Message - From: <[EMAIL PROTECTED]> To: Sent: Thursday, October 25, 2007 10:37 AM Subject: [gmx-users] solvate using genbox results in water in the centerofthe bilayer. How to edit pdb file contents in gromacs ? You can do it by two different methods. 1) You can increase the default VdW radii of the lipid atoms in /usr/local/ gromacs/share/top/vdwradii.dat file (path might be different from your system), say 0.5 for carbon, so genbox will not add the water inside the bilayer. Cleaner method is to: cp /usr/local/gromacs/share/top/vdwradii.dat ./vdwradii.dat and then modify the local file. but you will find a gap between lipid head groups and water molecules which can be resolved after some ps dynamics. (I personally have not yet got the success ;-) ) Do I understand you to say that for you the gap does not completely dissapear in <500ps? Did you use semiisotropic coupling? Otherwise it will be more difficult for this space to fill in. It should fill in really quite quickly (<<500ps)... has for me. 2) You can write a small script which can delete these water molecules, I wrote a script for the same if you need contact me offline. I have previously posted such a script. It takes 10-30 minutes to run since it's not sophisticated, but it does work very well. http://www.gromacs.org/pipermail/gmx-users/2006-May/021526.html I forgot to mention that in the previously referenced script there is an assumption that you use a 3 atom water molecule. If you use tip4p then you would want if [ "$count" = 3 ]; then count=0 fi to be changed to: if [ "$count" = 4 ]; then count=0 fi and etc for tip5p. Hope it will help Alok - Original Message - Hi I am using editconf to try to add water layers on either side of my bilayer. I use the following command: genbox -cp popc.gro -box 12.47820 12.35940 10.0 -o solvated.gro -cs spc216.gro -p topology.top However, because the center of the bilayer region is less dense, a lot of water molecules are created inside the bilayer. - How does one usually edit pdb files in gromacs, in terms of, for example, removing water molecules from the center of a bilayer ? Thank you -Maria ___ 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