RE: [gmx-users] Pull Code problems
Hi, If you pull without a reference, you will be doing nothing in the limit of slow pulling. For fast pulling you will be doing something. pull_start=yes pull_init1=0 will initialize set pull_init to the initial distance. Berk > Subject: RE: [gmx-users] Pull Code problems > From: gene...@gmail.com > To: gmx-users@gromacs.org > Date: Tue, 13 Jan 2009 19:59:38 +0300 > > OK, > > finally I try to simplify my question by revealing my final aim. > > I have a group that I want to pull out of my protein. I want only one > group to be pulled out in one direction. > > How could I do that? > SDA > > P.S. > In my understanding to do that I should leave reference group blank and > specify pull group only: > pull_group0= > pull_group1=r_535 > In this case grompp calculates initial distance from (0,0,0) to pull > group and sets the initial force to a very high value > (distance*force_constant) instead of 0. To correct this and to make the > initial pull rate = 0 I should set pull group to the center of > coordinates or set the initial position of the pull spring to the > position of the pull group. How should I do that? > > > On Tue, 2009-01-13 at 16:55 +0100, Berk Hess wrote: > > Hi, > > > > The pull option acts between COM's. Both COM's will move. > > If not, you would have a net force on the COM of the whole system. > > > > The AFM option is no longer there. > > I never understood what the difference between Umbrella and AFM was. > > But Umbrella (as well as constraint) should be able to do all things > > that were possible before (and more). > > > > Berk > > > > > Subject: Re: [gmx-users] Pull Code problems > > > From: gene...@gmail.com > > > To: gmx-users@gromacs.org > > > Date: Tue, 13 Jan 2009 18:44:36 +0300 > > > > > > OK, > > > I have a new problem. > > > I`ve started the simulation with the following pull parameters > > > > > > > > > ;---PULL CODE - > > > > > > pull<-->=<-> umbrella > > > pull_geometry<->= direction > > > pull_group0<-->= r_500 > > > pull_group1<--->= r_535 > > > pull_vec1<->= -1.306 1.355 -0.319 > > > pull_k1><-->= 1000 > > > pull_rate1<>= 1 ; nm/ps = 1 A/ns > > > > > > With such extreme pulling velocities I had my system teared apart in > > 100 > > > ps - that is OK I suggest. The problem is that pull group > > (pull_group1) > > > and reference group (pull_group0) were both pulled in opposite > > > directions - pull_vec1 and -(pull_vec1)?! > > > > > > 1/ In my best understanding the reference group is the one that > > stays > > > intact to track the movement of the group that is being pulled - > > pull > > > group. Then how could this happen in my system? What should I do to > > pull > > > only the pull_group1? > > > 2/ I was recomended to use AFM pull mode in gromacs 3. What is the > > new > > > name for AFM in gromacs 4? > > > > > > Thanks. > > > > > > > > > ___ > > > gmx-users mailing list gmx-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 gmx-users-requ...@gromacs.org. > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > __ > > Express yourself instantly with MSN Messenger! MSN Messenger > > ___ > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ What can you do with the new Windows Live? Find out http://www.microsoft.com/windows/windowslive/default.aspx___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Pull Code problems
OK, finally I try to simplify my question by revealing my final aim. I have a group that I want to pull out of my protein. I want only one group to be pulled out in one direction. How could I do that? SDA P.S. In my understanding to do that I should leave reference group blank and specify pull group only: pull_group0= pull_group1=r_535 In this case grompp calculates initial distance from (0,0,0) to pull group and sets the initial force to a very high value (distance*force_constant) instead of 0. To correct this and to make the initial pull rate = 0 I should set pull group to the center of coordinates or set the initial position of the pull spring to the position of the pull group. How should I do that? On Tue, 2009-01-13 at 16:55 +0100, Berk Hess wrote: > Hi, > > The pull option acts between COM's. Both COM's will move. > If not, you would have a net force on the COM of the whole system. > > The AFM option is no longer there. > I never understood what the difference between Umbrella and AFM was. > But Umbrella (as well as constraint) should be able to do all things > that were possible before (and more). > > Berk > > > Subject: Re: [gmx-users] Pull Code problems > > From: gene...@gmail.com > > To: gmx-users@gromacs.org > > Date: Tue, 13 Jan 2009 18:44:36 +0300 > > > > OK, > > I have a new problem. > > I`ve started the simulation with the following pull parameters > > > > > > ;---PULL CODE - > > > > pull<-->=<-> umbrella > > pull_geometry<->= direction > > pull_group0<-->= r_500 > > pull_group1<--->= r_535 > > pull_vec1<->= -1.306 1.355 -0.319 > > pull_k1><-->= 1000 > > pull_rate1<>= 1 ; nm/ps = 1 A/ns > > > > With such extreme pulling velocities I had my system teared apart in > 100 > > ps - that is OK I suggest. The problem is that pull group > (pull_group1) > > and reference group (pull_group0) were both pulled in opposite > > directions - pull_vec1 and -(pull_vec1)?! > > > > 1/ In my best understanding the reference group is the one that > stays > > intact to track the movement of the group that is being pulled - > pull > > group. Then how could this happen in my system? What should I do to > pull > > only the pull_group1? > > 2/ I was recomended to use AFM pull mode in gromacs 3. What is the > new > > name for AFM in gromacs 4? > > > > Thanks. > > > > > > ___ > > gmx-users mailing list gmx-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 gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > __ > Express yourself instantly with MSN Messenger! MSN Messenger ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Pull Code problems
Hi, The pull option acts between COM's. Both COM's will move. If not, you would have a net force on the COM of the whole system. The AFM option is no longer there. I never understood what the difference between Umbrella and AFM was. But Umbrella (as well as constraint) should be able to do all things that were possible before (and more). Berk > Subject: Re: [gmx-users] Pull Code problems > From: gene...@gmail.com > To: gmx-users@gromacs.org > Date: Tue, 13 Jan 2009 18:44:36 +0300 > > OK, > I have a new problem. > I`ve started the simulation with the following pull parameters > > > ;---PULL CODE - > > pull<-->=<-> umbrella > pull_geometry<->= direction > pull_group0<-->= r_500 > pull_group1<--->= r_535 > pull_vec1<->= -1.306 1.355 -0.319 > pull_k1><-->= 1000 > pull_rate1<>= 1 ; nm/ps = 1 A/ns > > With such extreme pulling velocities I had my system teared apart in 100 > ps - that is OK I suggest. The problem is that pull group (pull_group1) > and reference group (pull_group0) were both pulled in opposite > directions - pull_vec1 and -(pull_vec1)?! > > 1/ In my best understanding the reference group is the one that stays > intact to track the movement of the group that is being pulled - pull > group. Then how could this happen in my system? What should I do to pull > only the pull_group1? > 2/ I was recomended to use AFM pull mode in gromacs 3. What is the new > name for AFM in gromacs 4? > > Thanks. > > > ___ > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Pull Code problems
OK, I have a new problem. I`ve started the simulation with the following pull parameters ;---PULL CODE - pull<-->=<-> umbrella pull_geometry<->= direction pull_group0<-->= r_500 pull_group1<--->= r_535 pull_vec1<->= -1.306 1.355 -0.319 pull_k1><-->= 1000 pull_rate1<>= 1 ; nm/ps = 1 A/ns With such extreme pulling velocities I had my system teared apart in 100 ps - that is OK I suggest. The problem is that pull group (pull_group1) and reference group (pull_group0) were both pulled in opposite directions - pull_vec1 and -(pull_vec1)?! 1/ In my best understanding the reference group is the one that stays intact to track the movement of the group that is being pulled - pull group. Then how could this happen in my system? What should I do to pull only the pull_group1? 2/ I was recomended to use AFM pull mode in gromacs 3. What is the new name for AFM in gromacs 4? Thanks. ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Pull Code problems
Hi, pullx.xvg has the coordinates of group 0 and the distances of the other groups to group 0. pullf.xvg has the force of the umbrella potential which works along the direction vector you gave, this can be positive or negative depending on the direction. Berk > Subject: RE: [gmx-users] Pull Code problems > From: gene...@gmail.com > To: gmx-users@gromacs.org > Date: Tue, 13 Jan 2009 18:02:47 +0300 > > OK, > I did some homework and now I`m up to this: > > ;---PULL CODE - > > pull= umbrella > pull_geometry = direction > pull_group0 = r_500 > pull_group1 = r_535 > pull_vec1 = -1.306 1.355 -0.319 > pull_k1 = 1000 > pull_rate1 = 0.5 ; nm/ps Extreme parameters for extreme pulling > > Now I have two output files - pullx.xvg (-px option of mdrun) and > pullf.xvg (-pf option). > > pullx : > > @title "Pull COM" > @xaxis label "Time (ps)" > @yaxis label "Position (nm)" > @TYPE xy > @ view 0.15, 0.15, 0.75, 0.85 > @ legend on > @ legend box on > @ legend loctype view > @ legend 0.78, 0.8 > @ legend length 2 > @ s0 legend "0 X" > @ s1 legend "0 Y" > @ s2 legend "0 Z" > @ s3 legend "1 dX" > @ s4 legend "1 dY" > @ s5 legend "1 dZ" > 0.003.8995935.8163683.246447 > -0.285972 -0.132647 -0.183023 > 0.043.9011635.8121323.238992 > -0.292108 -0.141616 -0.180796 > 0.083.9025055.8062123.240236 > -0.314770 -0.143951 -0.186194 > 0.123.9053655.7979383.242384 > -0.336802 -0.142276 -0.197704 > 0.163.9088995.7948123.230687 > -0.342824 -0.160593 -0.178745 > 0.203.9101085.7975643.220754 > -0.340151 -0.161146 -0.152076 > > Am I correct about XYZ being position of the spring and dx dy dz - > group0-group1 distances? > > pullf : > > @title "Pull force" > @xaxis label "Time (ps)" > @yaxis label "Force (kJ/mol/nm)" > @TYPE xy > 0.00-132.088161 > 0.004000-128.605515 > 0.008000-125.008520 > 0.012000-121.568624 > 0.016000-118.475655 > 0.02-115.844403 > 0.024000-113.735184 > 0.028000-112.165522 > 0.032000-111.066433 > . ... > 1.232000409.573773 > 1.236000412.738957 > 1.24415.736038 > 1.244000418.446270 > 1.248000420.781766 > 1.252000422.747570 > 1.256000424.505472 > 1.26426.348269 > 1.264000428.568933 > 1.268000431.301610 > 1.272000434.467394 > > Why does it start with negative values? Should I use negative value for > pull_k1 (force constant)? > > Thank you for your answers, I appreciate your time. > > SDA > > > > On Tue, 2009-01-13 at 12:41 +0100, Berk Hess wrote: > > Hi, > > > > You don't indicate which xvg file was 0, I guess pullf.xvg. > > Could it be that you did not specify a force constant, meaning fc=0? > > > > Berk > > > > > From: gene...@gmail.com > > > To: gmx-users@gromacs.org > > > Date: Tue, 13 Jan 2009 14:26:47 +0300 > > > Subject: [gmx-users] Pull Code problems > > > > > > Hello, > > > > > > I am trying to run a pulling simulation with gromacs 4.0.2. > > > > > > I have appended the following pull code to the mdp file: > > > > > > ;---PULL CODE - > > > > > > pull = umbrella > > > pull_geometry = direction > > > pull_group0 = r_500 > > > pull_group1 = r_535 > > > pull_vec1 = -1.306 1.355 -0.319 > > > > > > Where r_500 is the group I am expecting to be pulled, > > > r_535 - the reference (the acid that is in fact in contact with > > > r_500) > > > > > > I have left all remaining parameters with default values. > > > > > > The problem is that NOTHING HAPPENED! XVG file had 0. throughout > > > simulation indicating that distance between pull group and reference > > > group was 0! > > > > > > 1/ What did I do wrong? > > > 2/ Is there any pull code tutorial for gromacs 4 (n
RE: [gmx-users] Pull Code problems
OK, I did some homework and now I`m up to this: ;---PULL CODE - pull= umbrella pull_geometry = direction pull_group0 = r_500 pull_group1 = r_535 pull_vec1 = -1.306 1.355 -0.319 pull_k1 = 1000 pull_rate1 = 0.5 ; nm/ps Extreme parameters for extreme pulling Now I have two output files - pullx.xvg (-px option of mdrun) and pullf.xvg (-pf option). pullx : @title "Pull COM" @xaxis label "Time (ps)" @yaxis label "Position (nm)" @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend "0 X" @ s1 legend "0 Y" @ s2 legend "0 Z" @ s3 legend "1 dX" @ s4 legend "1 dY" @ s5 legend "1 dZ" 0.003.8995935.8163683.246447 -0.285972 -0.132647 -0.183023 0.043.9011635.8121323.238992 -0.292108 -0.141616 -0.180796 0.083.9025055.8062123.240236 -0.314770 -0.143951 -0.186194 0.123.9053655.7979383.242384 -0.336802 -0.142276 -0.197704 0.163.9088995.7948123.230687 -0.342824 -0.160593 -0.178745 0.203.9101085.7975643.220754 -0.340151 -0.161146 -0.152076 Am I correct about XYZ being position of the spring and dx dy dz - group0-group1 distances? pullf : @title "Pull force" @xaxis label "Time (ps)" @yaxis label "Force (kJ/mol/nm)" @TYPE xy 0.00-132.088161 0.004000-128.605515 0.008000-125.008520 0.012000-121.568624 0.016000-118.475655 0.02-115.844403 0.024000-113.735184 0.028000-112.165522 0.032000-111.066433 . ... 1.232000409.573773 1.236000412.738957 1.24415.736038 1.244000418.446270 1.248000420.781766 1.252000422.747570 1.256000424.505472 1.26426.348269 1.264000428.568933 1.268000431.301610 1.272000434.467394 Why does it start with negative values? Should I use negative value for pull_k1 (force constant)? Thank you for your answers, I appreciate your time. SDA On Tue, 2009-01-13 at 12:41 +0100, Berk Hess wrote: > Hi, > > You don't indicate which xvg file was 0, I guess pullf.xvg. > Could it be that you did not specify a force constant, meaning fc=0? > > Berk > > > From: gene...@gmail.com > > To: gmx-users@gromacs.org > > Date: Tue, 13 Jan 2009 14:26:47 +0300 > > Subject: [gmx-users] Pull Code problems > > > > Hello, > > > > I am trying to run a pulling simulation with gromacs 4.0.2. > > > > I have appended the following pull code to the mdp file: > > > > ;---PULL CODE - > > > > pull = umbrella > > pull_geometry = direction > > pull_group0 = r_500 > > pull_group1 = r_535 > > pull_vec1 = -1.306 1.355 -0.319 > > > > Where r_500 is the group I am expecting to be pulled, > > r_535 - the reference (the acid that is in fact in contact with > > r_500) > > > > I have left all remaining parameters with default values. > > > > The problem is that NOTHING HAPPENED! XVG file had 0. throughout > > simulation indicating that distance between pull group and reference > > group was 0! > > > > 1/ What did I do wrong? > > 2/ Is there any pull code tutorial for gromacs 4 (not previous > > version)? > > > > Thank you! > > SDA > > > > ___ > > gmx-users mailing list gmx-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 gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > __ > What can you do with the new Windows Live? Find out ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Pull Code problems
Hi, You don't indicate which xvg file was 0, I guess pullf.xvg. Could it be that you did not specify a force constant, meaning fc=0? Berk > From: gene...@gmail.com > To: gmx-users@gromacs.org > Date: Tue, 13 Jan 2009 14:26:47 +0300 > Subject: [gmx-users] Pull Code problems > > Hello, > > I am trying to run a pulling simulation with gromacs 4.0.2. > > I have appended the following pull code to the mdp file: > > ;---PULL CODE - > > pull = umbrella > pull_geometry = direction > pull_group0 = r_500 > pull_group1 = r_535 > pull_vec1 = -1.306 1.355 -0.319 > > Where r_500 is the group I am expecting to be pulled, > r_535 - the reference (the acid that is in fact in contact with > r_500) > > I have left all remaining parameters with default values. > > The problem is that NOTHING HAPPENED! XVG file had 0. throughout > simulation indicating that distance between pull group and reference > group was 0! > > 1/ What did I do wrong? > 2/ Is there any pull code tutorial for gromacs 4 (not previous > version)? > > Thank you! > SDA > > ___ > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ What can you do with the new Windows Live? Find out http://www.microsoft.com/windows/windowslive/default.aspx___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
