Re: [gmx-users] Re: REMD analysis
Dear Sir, I tried a lot to understand the meaning and relation between the .log file and relica_index file, but I was not able to break the code. I tried to look into gmx forum for some clue, but didn't find any. So, if possible can you explain it ... Replica exchange at step 1000 time 2 Repl 0 - 1 dE = -1.067e+00 Repl ex 0 x 123456789 10 11 12 x 13 Repl pr 1.0 .01 .68 .21 .05 .09 .26 Replica exchange at step 2000 time 4 Repl ex 01 x 23456789 10 11 12 13 Repl pr.91 .32 .00 .07 .18 .08 output of replica_index.xvg 0 0123456789 10 11 12 13 2 1023456789 10 11 13 12 4 1203456789 10 11 13 12 On Thu, May 23, 2013 at 11:20 PM, Mark Abraham mark.j.abra...@gmail.comwrote: Looked fine On Thu, May 23, 2013 at 4:13 PM, bharat gupta bharat.85.m...@gmail.com wrote: Sir, What about the description of replica_temp file that I posted in last mail. I think that's correct ... If you can comment on that, I can move on with replica_index file... On Thu, May 23, 2013 at 10:58 PM, Mark Abraham mark.j.abra...@gmail.com wrote: It's a demux. One might want trajectories to be at constant temperature, or constant replica. The two files define the (mutually inverse) mappings between those representations. So one file tells you which replica is at each temperature, and the other which temperature holds each replica. Nobody's ever written down anything about which is which, so like I said a week back, look at the first few exchanges, see how those are represented in the files, and decide for yourself which file's columns/rows have useful information you want to look at. And do write that decision down! :-) Mark On Thu, May 23, 2013 at 2:55 PM, simula_460 bharat.85.m...@gmail.com wrote: I checked the md.log and replica_temp.xvg file , what I understood is that the 'x' means swapping and replica are written this way. For eg. Replica exchange at step 1000 time 2 Repl 0 - 1 dE = -1.067e+00 Repl ex 0 x 123456789 10 11 12 x 13 Repl pr 1.0 .01 .68 .21 .05 .09 .26 output in replica_temp file will be 1 0 2 3 4 5 6 7 8 9 10 11 13 12 It means that replica 1 at higher temp. exchange with the one in lower temp 0. Replica exchange at step 2000 time 4 Repl ex 01 x 23456789 10 11 12 13 Repl pr.91 .32 .00 .07 .18 .08 output in replica_temp file will be 1 0 2 3 4 5 6 7 8 9 10 11 13 12 2 0 1 3 4 5 6 7 8 9 10 11 13 12 [order is from low to high temp] But I am not able to understand for replica_index file :- for the above two time steps here's the output :- 0 0123456789 10 11 12 13 2 1023456789 10 11 13 12 4 1203456789 10 11 13 12 The time step four is different here, I don't know why ?? Ideally the output should be same in both files, I suppose ?? Also, I tried to plot for each column separately , here I want to clarify that whether each column represents the time evolution of each replica over time. For eg. the second column should represent the temp evolution for replica No. 0 wrt to time. Presuming that I understood it correctly, I plotted the temp. evolution over time of all replicas separately . Here's the replica_temp plot for replicas 0 to 13. https://www.dropbox.com/s/0c8gp584v1hvlbx/replica_temp.png -- View this message in context: http://gromacs.5086.x6.nabble.com/REMD-analysis-tp5008199p5008481.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to
Re: [gmx-users] Re: REMD analysis
At time 0 we have an set of replicas and an (ordered) set of ensembles. We could label these however we liked, but for (in)convenience we use 0-(n-1) for both. The rows of the matrices in the *.xvg files change with time. At time 2, replicas in ensemble 0 and 1 have exchanged, so replica 0 is now in ensemble 1. At time 4, replicas in ensemble 1 and 2 have exchanged. So replica 0 is now in ensemble 2, which is expressed by 0 in the third column of the third row of replica_index.xvg. The same condition is expressed by the first column of the third row of replica_temp.xvg, where you will find 2, also expressing that replica 0 is in ensemble 2 at time 4. The columns of the two matrices allow you to see either the profile of which replica was in this ensemble at which time, or which ensemble this replica was in at which time. Mark On Fri, May 24, 2013 at 8:43 AM, bharat gupta bharat.85.m...@gmail.comwrote: Dear Sir, I tried a lot to understand the meaning and relation between the .log file and relica_index file, but I was not able to break the code. I tried to look into gmx forum for some clue, but didn't find any. So, if possible can you explain it ... Replica exchange at step 1000 time 2 Repl 0 - 1 dE = -1.067e+00 Repl ex 0 x 123456789 10 11 12 x 13 Repl pr 1.0 .01 .68 .21 .05 .09 .26 Replica exchange at step 2000 time 4 Repl ex 01 x 23456789 10 11 12 13 Repl pr.91 .32 .00 .07 .18 .08 output of replica_index.xvg 0 0123456789 10 11 12 13 2 1023456789 10 11 13 12 4 1203456789 10 11 13 12 On Thu, May 23, 2013 at 11:20 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Looked fine On Thu, May 23, 2013 at 4:13 PM, bharat gupta bharat.85.m...@gmail.com wrote: Sir, What about the description of replica_temp file that I posted in last mail. I think that's correct ... If you can comment on that, I can move on with replica_index file... On Thu, May 23, 2013 at 10:58 PM, Mark Abraham mark.j.abra...@gmail.com wrote: It's a demux. One might want trajectories to be at constant temperature, or constant replica. The two files define the (mutually inverse) mappings between those representations. So one file tells you which replica is at each temperature, and the other which temperature holds each replica. Nobody's ever written down anything about which is which, so like I said a week back, look at the first few exchanges, see how those are represented in the files, and decide for yourself which file's columns/rows have useful information you want to look at. And do write that decision down! :-) Mark On Thu, May 23, 2013 at 2:55 PM, simula_460 bharat.85.m...@gmail.com wrote: I checked the md.log and replica_temp.xvg file , what I understood is that the 'x' means swapping and replica are written this way. For eg. Replica exchange at step 1000 time 2 Repl 0 - 1 dE = -1.067e+00 Repl ex 0 x 123456789 10 11 12 x 13 Repl pr 1.0 .01 .68 .21 .05 .09 .26 output in replica_temp file will be 1 0 2 3 4 5 6 7 8 9 10 11 13 12 It means that replica 1 at higher temp. exchange with the one in lower temp 0. Replica exchange at step 2000 time 4 Repl ex 01 x 23456789 10 11 12 13 Repl pr.91 .32 .00 .07 .18 .08 output in replica_temp file will be 1 0 2 3 4 5 6 7 8 9 10 11 13 12 2 0 1 3 4 5 6 7 8 9 10 11 13 12 [order is from low to high temp] But I am not able to understand for replica_index file :- for the above two time steps here's the output :- 0 0123456789 10 11 12 13 2 1023456789 10 11 13 12 4 1203456789 10 11 13 12 The time step four is different here, I don't know why ?? Ideally the output should be same in both files, I suppose ?? Also, I tried to plot for each column separately , here I want to clarify that whether each column represents the time evolution of each replica over time. For eg. the second column should represent the temp evolution for replica No. 0 wrt to time. Presuming that I understood it correctly, I plotted the temp. evolution over time of all replicas separately . Here's the replica_temp plot for replicas 0
Re: [gmx-users] Re: REMD analysis
Dear Sir, Thank you for your detailed response to my query. I understood the concept of ordered arrangement of ensembles in replica_index.xvg. But I have a doubt, you said that *At time 4, replicas in ensemble 1 and 2 have exchanged. So replica 0 is now in ensemble 2, which is expressed by 0 in the third column* *of the third row of replica_index.xvg.* This is fine , as the output of replica_index is :- 4 12*0 * 3456789 10 11 13 12 But, i didn't understand this The same condition is expressed by the first column of the third row of replica_temp.xvg, where you will find 2, also expressing that replica 0 is in ensemble 2 at time 4. Here's the output for replica_temp . The first column third row is 2, its ok, but, its shows that replica 0 is in ensemble 1 instead of 2. 4 2013456789 10 11 13 12 In addition to this, in my last mail I showed the temp graph for all replicas. (https://www.dropbox.com/s/0c8gp584v1hvlbx/replica_temp.png) . Not all replicas visit all the temperatures, but some of them visit all the temperatures. Is it sufficient to move with the further analysis , as in some papers they show that some replicas visit all the temp which means that the sufficient sampling has been achieved. In my case this is true for some of the replicas and the average acceptance ratio achieved was 0.22 ?? On Fri, May 24, 2013 at 5:07 PM, Mark Abraham mark.j.abra...@gmail.comwrote: At time 0 we have an set of replicas and an (ordered) set of ensembles. We could label these however we liked, but for (in)convenience we use 0-(n-1) for both. The rows of the matrices in the *.xvg files change with time. At time 2, replicas in ensemble 0 and 1 have exchanged, so replica 0 is now in ensemble 1. At time 4, replicas in ensemble 1 and 2 have exchanged. So replica 0 is now in ensemble 2, which is expressed by 0 in the third column of the third row of replica_index.xvg. The same condition is expressed by the first column of the third row of replica_temp.xvg, where you will find 2, also expressing that replica 0 is in ensemble 2 at time 4. The columns of the two matrices allow you to see either the profile of which replica was in this ensemble at which time, or which ensemble this replica was in at which time. Mark On Fri, May 24, 2013 at 8:43 AM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, I tried a lot to understand the meaning and relation between the .log file and relica_index file, but I was not able to break the code. I tried to look into gmx forum for some clue, but didn't find any. So, if possible can you explain it ... Replica exchange at step 1000 time 2 Repl 0 - 1 dE = -1.067e+00 Repl ex 0 x 123456789 10 11 12 x 13 Repl pr 1.0 .01 .68 .21 .05 .09 .26 Replica exchange at step 2000 time 4 Repl ex 01 x 23456789 10 11 12 13 Repl pr.91 .32 .00 .07 .18 .08 output of replica_index.xvg 0 0123456789 10 11 12 13 2 1023456789 10 11 13 12 4 1203456789 10 11 13 12 On Thu, May 23, 2013 at 11:20 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Looked fine On Thu, May 23, 2013 at 4:13 PM, bharat gupta bharat.85.m...@gmail.com wrote: Sir, What about the description of replica_temp file that I posted in last mail. I think that's correct ... If you can comment on that, I can move on with replica_index file... On Thu, May 23, 2013 at 10:58 PM, Mark Abraham mark.j.abra...@gmail.com wrote: It's a demux. One might want trajectories to be at constant temperature, or constant replica. The two files define the (mutually inverse) mappings between those representations. So one file tells you which replica is at each temperature, and the other which temperature holds each replica. Nobody's ever written down anything about which is which, so like I said a week back, look at the first few exchanges, see how those are represented in the files, and decide for yourself which file's columns/rows have useful information you want to look at. And do write that decision down! :-) Mark On Thu, May 23, 2013 at 2:55 PM, simula_460 bharat.85.m...@gmail.com wrote: I checked the md.log and replica_temp.xvg file , what I understood is that the 'x' means swapping and replica are written this way. For eg. Replica exchange at step 1000 time 2 Repl 0 - 1 dE = -1.067e+00 Repl ex 0 x 123456789 10 11
Re: [gmx-users] Re: REMD analysis
On Fri, May 24, 2013 at 10:44 AM, bharat gupta bharat.85.m...@gmail.comwrote: Dear Sir, Thank you for your detailed response to my query. I understood the concept of ordered arrangement of ensembles in replica_index.xvg. But I have a doubt, you said that *At time 4, replicas in ensemble 1 and 2 have exchanged. So replica 0 is now in ensemble 2, which is expressed by 0 in the third column* *of the third row of replica_index.xvg.* This is fine , as the output of replica_index is :- 4 12*0 * 3456789 10 11 13 12 But, i didn't understand this The same condition is expressed by the first column of the third row of replica_temp.xvg, where you will find 2, also expressing that replica 0 is in ensemble 2 at time 4. Here's the output for replica_temp . The first column third row is 2, its ok, but, its shows that replica 0 is in ensemble 1 instead of 2. No, if the rows of both matrices describe time, and there are two different matrices for the same exchange set, then the information described by a column must differ, like I said last email. You are applying the same interpretation to a column from either matrix. 4 2013456789 10 11 13 12 In addition to this, in my last mail I showed the temp graph for all replicas. (https://www.dropbox.com/s/0c8gp584v1hvlbx/replica_temp.png) . Not all replicas visit all the temperatures, but some of them visit all the temperatures. Is it sufficient to move with the further analysis , as in some papers they show that some replicas visit all the temp which means that the sufficient sampling has been achieved. In my case this is true for some of the replicas and the average acceptance ratio achieved was 0.22 ?? I've answered this question several times. Each replica merely visiting each temperature means nothing for converged sampling. There's lots of literature here, including stuff by me ;-) A balance of replicas visiting ensembles is necessary but not sufficient for the kind of replica flow that would be necessary for generalized convergence. One can shrug one's shoulders at some point and say things are probably as good as they'll get for reasonable cost, but your reviewer might disagree with you. Convergence of sampling at a single temperature can be assessed in a similar way as for non-REMD simulations, caveat that the exchange events pretty much stop you using metrics based on correlation time. If you want to know how to do things properly, you need to do some reading. Mark On Fri, May 24, 2013 at 5:07 PM, Mark Abraham mark.j.abra...@gmail.com wrote: At time 0 we have an set of replicas and an (ordered) set of ensembles. We could label these however we liked, but for (in)convenience we use 0-(n-1) for both. The rows of the matrices in the *.xvg files change with time. At time 2, replicas in ensemble 0 and 1 have exchanged, so replica 0 is now in ensemble 1. At time 4, replicas in ensemble 1 and 2 have exchanged. So replica 0 is now in ensemble 2, which is expressed by 0 in the third column of the third row of replica_index.xvg. The same condition is expressed by the first column of the third row of replica_temp.xvg, where you will find 2, also expressing that replica 0 is in ensemble 2 at time 4. The columns of the two matrices allow you to see either the profile of which replica was in this ensemble at which time, or which ensemble this replica was in at which time. Mark On Fri, May 24, 2013 at 8:43 AM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, I tried a lot to understand the meaning and relation between the .log file and relica_index file, but I was not able to break the code. I tried to look into gmx forum for some clue, but didn't find any. So, if possible can you explain it ... Replica exchange at step 1000 time 2 Repl 0 - 1 dE = -1.067e+00 Repl ex 0 x 123456789 10 11 12 x 13 Repl pr 1.0 .01 .68 .21 .05 .09 .26 Replica exchange at step 2000 time 4 Repl ex 01 x 23456789 10 11 12 13 Repl pr.91 .32 .00 .07 .18 .08 output of replica_index.xvg 0 0123456789 10 11 12 13 2 1023456789 10 11 13 12 4 1203456789 10 11 13 12 On Thu, May 23, 2013 at 11:20 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Looked fine On Thu, May 23, 2013 at 4:13 PM, bharat gupta bharat.85.m...@gmail.com wrote: Sir, What about the description of replica_temp file that I posted in last mail. I think that's correct ... If you can comment on that, I can move
Re: [gmx-users] Re: REMD analysis
Hi to everybody, Bharat, maybe i didn't follow exactly the wole tale, but is it possible you are running xmgrace without the -nxy option? You are probably visualizing the data related the 1st replica several times! Francesco 2013/5/24 Mark Abraham mark.j.abra...@gmail.com On Fri, May 24, 2013 at 10:44 AM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, Thank you for your detailed response to my query. I understood the concept of ordered arrangement of ensembles in replica_index.xvg. But I have a doubt, you said that *At time 4, replicas in ensemble 1 and 2 have exchanged. So replica 0 is now in ensemble 2, which is expressed by 0 in the third column* *of the third row of replica_index.xvg.* This is fine , as the output of replica_index is :- 4 12*0 * 3456789 10 11 13 12 But, i didn't understand this The same condition is expressed by the first column of the third row of replica_temp.xvg, where you will find 2, also expressing that replica 0 is in ensemble 2 at time 4. Here's the output for replica_temp . The first column third row is 2, its ok, but, its shows that replica 0 is in ensemble 1 instead of 2. No, if the rows of both matrices describe time, and there are two different matrices for the same exchange set, then the information described by a column must differ, like I said last email. You are applying the same interpretation to a column from either matrix. 4 2013456789 10 11 13 12 In addition to this, in my last mail I showed the temp graph for all replicas. (https://www.dropbox.com/s/0c8gp584v1hvlbx/replica_temp.png) . Not all replicas visit all the temperatures, but some of them visit all the temperatures. Is it sufficient to move with the further analysis , as in some papers they show that some replicas visit all the temp which means that the sufficient sampling has been achieved. In my case this is true for some of the replicas and the average acceptance ratio achieved was 0.22 ?? I've answered this question several times. Each replica merely visiting each temperature means nothing for converged sampling. There's lots of literature here, including stuff by me ;-) A balance of replicas visiting ensembles is necessary but not sufficient for the kind of replica flow that would be necessary for generalized convergence. One can shrug one's shoulders at some point and say things are probably as good as they'll get for reasonable cost, but your reviewer might disagree with you. Convergence of sampling at a single temperature can be assessed in a similar way as for non-REMD simulations, caveat that the exchange events pretty much stop you using metrics based on correlation time. If you want to know how to do things properly, you need to do some reading. Mark On Fri, May 24, 2013 at 5:07 PM, Mark Abraham mark.j.abra...@gmail.com wrote: At time 0 we have an set of replicas and an (ordered) set of ensembles. We could label these however we liked, but for (in)convenience we use 0-(n-1) for both. The rows of the matrices in the *.xvg files change with time. At time 2, replicas in ensemble 0 and 1 have exchanged, so replica 0 is now in ensemble 1. At time 4, replicas in ensemble 1 and 2 have exchanged. So replica 0 is now in ensemble 2, which is expressed by 0 in the third column of the third row of replica_index.xvg. The same condition is expressed by the first column of the third row of replica_temp.xvg, where you will find 2, also expressing that replica 0 is in ensemble 2 at time 4. The columns of the two matrices allow you to see either the profile of which replica was in this ensemble at which time, or which ensemble this replica was in at which time. Mark On Fri, May 24, 2013 at 8:43 AM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, I tried a lot to understand the meaning and relation between the .log file and relica_index file, but I was not able to break the code. I tried to look into gmx forum for some clue, but didn't find any. So, if possible can you explain it ... Replica exchange at step 1000 time 2 Repl 0 - 1 dE = -1.067e+00 Repl ex 0 x 123456789 10 11 12 x 13 Repl pr 1.0 .01 .68 .21 .05 .09 .26 Replica exchange at step 2000 time 4 Repl ex 01 x 23456789 10 11 12 13 Repl pr.91 .32 .00 .07 .18 .08 output of replica_index.xvg 0 0123456789 10 11 12 13 2 1023456789 10 11 13 12 4 1203456789
Re: [gmx-users] Re: REMD analysis
Dear Sir, Thank you for the advice. I have not understood the things properly, especially the convergence of REMD. I got two relevant papers : 1. Convergence of replica exchange molecular dynamics 2. Convergence and sampling efficiency in replica exchange simulations of peptide folding in explicit solvent. If you can provide better reference then this ... Thank you francesco for the option. Indeed I was missing a a very imp. option while plotting the data. On Fri, May 24, 2013 at 7:40 PM, francesco oteri francesco.ot...@gmail.comwrote: Hi to everybody, Bharat, maybe i didn't follow exactly the wole tale, but is it possible you are running xmgrace without the -nxy option? You are probably visualizing the data related the 1st replica several times! Francesco 2013/5/24 Mark Abraham mark.j.abra...@gmail.com On Fri, May 24, 2013 at 10:44 AM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, Thank you for your detailed response to my query. I understood the concept of ordered arrangement of ensembles in replica_index.xvg. But I have a doubt, you said that *At time 4, replicas in ensemble 1 and 2 have exchanged. So replica 0 is now in ensemble 2, which is expressed by 0 in the third column* *of the third row of replica_index.xvg.* This is fine , as the output of replica_index is :- 4 12*0 * 3456789 10 11 13 12 But, i didn't understand this The same condition is expressed by the first column of the third row of replica_temp.xvg, where you will find 2, also expressing that replica 0 is in ensemble 2 at time 4. Here's the output for replica_temp . The first column third row is 2, its ok, but, its shows that replica 0 is in ensemble 1 instead of 2. No, if the rows of both matrices describe time, and there are two different matrices for the same exchange set, then the information described by a column must differ, like I said last email. You are applying the same interpretation to a column from either matrix. 4 2013456789 10 11 13 12 In addition to this, in my last mail I showed the temp graph for all replicas. (https://www.dropbox.com/s/0c8gp584v1hvlbx/replica_temp.png) . Not all replicas visit all the temperatures, but some of them visit all the temperatures. Is it sufficient to move with the further analysis , as in some papers they show that some replicas visit all the temp which means that the sufficient sampling has been achieved. In my case this is true for some of the replicas and the average acceptance ratio achieved was 0.22 ?? I've answered this question several times. Each replica merely visiting each temperature means nothing for converged sampling. There's lots of literature here, including stuff by me ;-) A balance of replicas visiting ensembles is necessary but not sufficient for the kind of replica flow that would be necessary for generalized convergence. One can shrug one's shoulders at some point and say things are probably as good as they'll get for reasonable cost, but your reviewer might disagree with you. Convergence of sampling at a single temperature can be assessed in a similar way as for non-REMD simulations, caveat that the exchange events pretty much stop you using metrics based on correlation time. If you want to know how to do things properly, you need to do some reading. Mark On Fri, May 24, 2013 at 5:07 PM, Mark Abraham mark.j.abra...@gmail.com wrote: At time 0 we have an set of replicas and an (ordered) set of ensembles. We could label these however we liked, but for (in)convenience we use 0-(n-1) for both. The rows of the matrices in the *.xvg files change with time. At time 2, replicas in ensemble 0 and 1 have exchanged, so replica 0 is now in ensemble 1. At time 4, replicas in ensemble 1 and 2 have exchanged. So replica 0 is now in ensemble 2, which is expressed by 0 in the third column of the third row of replica_index.xvg. The same condition is expressed by the first column of the third row of replica_temp.xvg, where you will find 2, also expressing that replica 0 is in ensemble 2 at time 4. The columns of the two matrices allow you to see either the profile of which replica was in this ensemble at which time, or which ensemble this replica was in at which time. Mark On Fri, May 24, 2013 at 8:43 AM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, I tried a lot to understand the meaning and relation between the .log file and relica_index file, but I was not able to break the code. I tried to look into gmx forum for some clue, but didn't find any. So, if possible can you explain it ... Replica exchange
Re: [gmx-users] Re: REMD analysis
On Wed, May 22, 2013 at 2:19 AM, bharat gupta bharat.85.m...@gmail.comwrote: Dear Sir, I performed another round of trial with different set of temperature and I got the avg accp. ration around 0.22. Here's the temp. dist. that I used : 250 268 288 308 331 355 380 408 438 469 503 540 579 621 I then checked the replica_index and replica_temp files for each replica individually. The plots are exactly similar for all the replicas, as an eg. here's the link for first three replicas . https://www.dropbox.com/s/cuydj010wh2hgkt/replica_index0.png https://www.dropbox.com/s/q01wluh8wxlcxs8/replica_index1.png https://www.dropbox.com/s/cm9f8qo1afo6w4k/replica_index2.png https://www.dropbox.com/s/gkbu0g0e1r37l57/replica_temp0.png https://www.dropbox.com/s/sffq8rwghjublu0/replica_temp1.png https://www.dropbox.com/s/ulccw8xabj66ktm/replica_temp2.png These are the same data. Whatever you are doing to generate them isn't what you think you're doing :-) Mark I checked the PE overlap also, that looks fine ( https://www.dropbox.com/s/0qf06of9lp1m51d/pe_overlap.png) I checked for the temp. dist. which also looks fine to me . https://www.dropbox.com/s/ed66uop16blgqwa/temp_dist.png I don't know why all plots are similar ?? Is this related to wrong settings in mdp file. Here's the mdp file that I am using for production run. I changed ref_t for each replica in the mdp file. I suspect that I am doing something wrong somewhere ... define = -DPOSRESHELIX ; -DFLEXIBLE -DPOSRES constraints = all-bonds integrator = md dt = 0.002 ; ps nsteps = 2500; 5 ps = 50 ns nstcomm = 10 nstcalcenergy = 10 nstxout = 1000 ; frequency to write coordinates to output trajectory nstvout = 0 ; frequency to write velocities to output trajectory; the last velocities are always written nstfout = 0 ; frequency to write forces to output trajectory nstlog = 1000 ; frequency to write energies to log file nstenergy = 1000 ; frequency to write energies to edr file vdwtype = cut-off coulombtype = cut-off pbc = no nstlist = 0 ns_type = simple rlist = 0 ; this means all-vs-all (no cut-off), which gets expensive for bigger systems rcoulomb= 0 rvdw= 0 comm-mode = angular comm-grps = system optimize_fft= yes ; V-rescale temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 tc_grps = system ref_t = 250 ; Pressure coupling is off Pcoupl = no ; Generate velocites is on gen_vel = yes gen_temp= 300 gen_seed= -1 ; ; Implicit solvent ; implicit_solvent= GBSA gb_algorithm= Still ; HCT ; OBC nstgbradii = 1 rgbradii= 0 ; [nm] Cut-off for the calculation of the Born radii. Currently must be equal to rlist gb_epsilon_solvent = 78.5; Dielectric constant for the implicit solvent ; gb_saltconc = 0 ; Salt concentration for implicit solvent models, currently not used sa_algorithm= Ace-approximation sa_surface_tension = 0.005 It will be helpful if you provide your comments... Regards -- BHARAT -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Re: REMD analysis
Dear Sir, Thank you for your reply. But I used the command demux.pl md$.log , where $= No. of replica. I get the same plot every time. Sorry to ask this , but where am I going wrong ?? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: REMD analysis
Look at those files. Use diff. They're all the same. Your plots are probably all showing the first column of each. You want to look at each column. (And even then the best it can show is that your simulation is not clearly inadequate.) Mark On Thu, May 23, 2013 at 8:48 AM, bharat gupta bharat.85.m...@gmail.comwrote: Dear Sir, Thank you for your reply. But I used the command demux.pl md$.log , where $= No. of replica. I get the same plot every time. Sorry to ask this , but where am I going wrong ?? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: REMD analysis
I checked the first 5 md.log files, and the data is exactly the same in all of them Does it mean there could be problem with demux.pl On Thu, May 23, 2013 at 3:53 PM, Mark Abraham mark.j.abra...@gmail.comwrote: Look at those files. Use diff. They're all the same. Your plots are probably all showing the first column of each. You want to look at each column. (And even then the best it can show is that your simulation is not clearly inadequate.) Mark On Thu, May 23, 2013 at 8:48 AM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, Thank you for your reply. But I used the command demux.pl md$.log , where $= No. of replica. I get the same plot every time. Sorry to ask this , but where am I going wrong ?? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Re: REMD analysis
Each md.log has all the information about all replica exchanges, as you can see. I suggested you look at your .log and .xvg files a week ago ;-) There's no problem if a script post-processes all the identical information from each .log file. Mark On Thu, May 23, 2013 at 9:01 AM, bharat gupta bharat.85.m...@gmail.comwrote: I checked the first 5 md.log files, and the data is exactly the same in all of them Does it mean there could be problem with demux.pl On Thu, May 23, 2013 at 3:53 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Look at those files. Use diff. They're all the same. Your plots are probably all showing the first column of each. You want to look at each column. (And even then the best it can show is that your simulation is not clearly inadequate.) Mark On Thu, May 23, 2013 at 8:48 AM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, Thank you for your reply. But I used the command demux.pl md$.log , where $= No. of replica. I get the same plot every time. Sorry to ask this , but where am I going wrong ?? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Re: REMD analysis
Dear Sir, I checked the md.log and replica_temp.xvg file , what I understood is that the 'x' means swapping and replica are written that way. For eg. Replica exchange at step 1000 time 2 Repl 0 - 1 dE = -1.067e+00 Repl ex 0 x 123456789 10 11 12 x 13 Repl pr 1.0 .01 .68 .21 .05 .09 .26 output in replica_temp file will be 1 0 2 3 4 5 6 7 8 9 10 11 13 12 It means that replica 1 at higher temp. exchange with the one in lower temp 0. Replica exchange at step 2000 time 4 Repl ex 01 x 23456789 10 11 12 13 Repl pr.91 .32 .00 .07 .18 .08 output in replica_temp file will be 1 0 2 3 4 5 6 7 8 9 10 11 13 12 2 0 1 3 4 5 6 7 8 9 10 11 13 12 [order is from low to high temp] But I am not able to understand for replica_index file :- for the above two time steps here's the output :- 0 0123456789 10 11 12 13 2 1023456789 10 11 13 12 4 1203456789 10 11 13 12 The time step four is different here, I don't know why ?? Ideally the output should be same in both files, I suppose ?? Also, I tried to plot for each column separately , here I want to clarify that whether each column represents the time evolution of each replica over time. For eg. the second column should represent the temp evolution for replica No. 0 wrt to time. Presuming that I understood it correctly, I plotted the temp. evolution over time of all replicas separately . Here's the replica_temp plot for replicas 0 to 13. https://www.dropbox.com/s/0c8gp584v1hvlbx/replica_temp.png On Thu, May 23, 2013 at 5:21 PM, Mark Abraham mark.j.abra...@gmail.comwrote: Each md.log has all the information about all replica exchanges, as you can see. I suggested you look at your .log and .xvg files a week ago ;-) There's no problem if a script post-processes all the identical information from each .log file. Mark On Thu, May 23, 2013 at 9:01 AM, bharat gupta bharat.85.m...@gmail.com wrote: I checked the first 5 md.log files, and the data is exactly the same in all of them Does it mean there could be problem with demux.pl On Thu, May 23, 2013 at 3:53 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Look at those files. Use diff. They're all the same. Your plots are probably all showing the first column of each. You want to look at each column. (And even then the best it can show is that your simulation is not clearly inadequate.) Mark On Thu, May 23, 2013 at 8:48 AM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, Thank you for your reply. But I used the command demux.pl md$.log , where $= No. of replica. I get the same plot every time. Sorry to ask this , but where am I going wrong ?? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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
Re: [gmx-users] Re: REMD analysis
It's a demux. One might want trajectories to be at constant temperature, or constant replica. The two files define the (mutually inverse) mappings between those representations. So one file tells you which replica is at each temperature, and the other which temperature holds each replica. Nobody's ever written down anything about which is which, so like I said a week back, look at the first few exchanges, see how those are represented in the files, and decide for yourself which file's columns/rows have useful information you want to look at. And do write that decision down! :-) Mark On Thu, May 23, 2013 at 2:55 PM, simula_460 bharat.85.m...@gmail.comwrote: I checked the md.log and replica_temp.xvg file , what I understood is that the 'x' means swapping and replica are written this way. For eg. Replica exchange at step 1000 time 2 Repl 0 - 1 dE = -1.067e+00 Repl ex 0 x 123456789 10 11 12 x 13 Repl pr 1.0 .01 .68 .21 .05 .09 .26 output in replica_temp file will be 1 0 2 3 4 5 6 7 8 9 10 11 13 12 It means that replica 1 at higher temp. exchange with the one in lower temp 0. Replica exchange at step 2000 time 4 Repl ex 01 x 23456789 10 11 12 13 Repl pr.91 .32 .00 .07 .18 .08 output in replica_temp file will be 1 0 2 3 4 5 6 7 8 9 10 11 13 12 2 0 1 3 4 5 6 7 8 9 10 11 13 12 [order is from low to high temp] But I am not able to understand for replica_index file :- for the above two time steps here's the output :- 0 0123456789 10 11 12 13 2 1023456789 10 11 13 12 4 1203456789 10 11 13 12 The time step four is different here, I don't know why ?? Ideally the output should be same in both files, I suppose ?? Also, I tried to plot for each column separately , here I want to clarify that whether each column represents the time evolution of each replica over time. For eg. the second column should represent the temp evolution for replica No. 0 wrt to time. Presuming that I understood it correctly, I plotted the temp. evolution over time of all replicas separately . Here's the replica_temp plot for replicas 0 to 13. https://www.dropbox.com/s/0c8gp584v1hvlbx/replica_temp.png -- View this message in context: http://gromacs.5086.x6.nabble.com/REMD-analysis-tp5008199p5008481.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Re: REMD analysis
Sir, What about the description of replica_temp file that I posted in last mail. I think that's correct ... If you can comment on that, I can move on with replica_index file... On Thu, May 23, 2013 at 10:58 PM, Mark Abraham mark.j.abra...@gmail.comwrote: It's a demux. One might want trajectories to be at constant temperature, or constant replica. The two files define the (mutually inverse) mappings between those representations. So one file tells you which replica is at each temperature, and the other which temperature holds each replica. Nobody's ever written down anything about which is which, so like I said a week back, look at the first few exchanges, see how those are represented in the files, and decide for yourself which file's columns/rows have useful information you want to look at. And do write that decision down! :-) Mark On Thu, May 23, 2013 at 2:55 PM, simula_460 bharat.85.m...@gmail.com wrote: I checked the md.log and replica_temp.xvg file , what I understood is that the 'x' means swapping and replica are written this way. For eg. Replica exchange at step 1000 time 2 Repl 0 - 1 dE = -1.067e+00 Repl ex 0 x 123456789 10 11 12 x 13 Repl pr 1.0 .01 .68 .21 .05 .09 .26 output in replica_temp file will be 1 0 2 3 4 5 6 7 8 9 10 11 13 12 It means that replica 1 at higher temp. exchange with the one in lower temp 0. Replica exchange at step 2000 time 4 Repl ex 01 x 23456789 10 11 12 13 Repl pr.91 .32 .00 .07 .18 .08 output in replica_temp file will be 1 0 2 3 4 5 6 7 8 9 10 11 13 12 2 0 1 3 4 5 6 7 8 9 10 11 13 12 [order is from low to high temp] But I am not able to understand for replica_index file :- for the above two time steps here's the output :- 0 0123456789 10 11 12 13 2 1023456789 10 11 13 12 4 1203456789 10 11 13 12 The time step four is different here, I don't know why ?? Ideally the output should be same in both files, I suppose ?? Also, I tried to plot for each column separately , here I want to clarify that whether each column represents the time evolution of each replica over time. For eg. the second column should represent the temp evolution for replica No. 0 wrt to time. Presuming that I understood it correctly, I plotted the temp. evolution over time of all replicas separately . Here's the replica_temp plot for replicas 0 to 13. https://www.dropbox.com/s/0c8gp584v1hvlbx/replica_temp.png -- View this message in context: http://gromacs.5086.x6.nabble.com/REMD-analysis-tp5008199p5008481.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Re: REMD analysis
Looked fine On Thu, May 23, 2013 at 4:13 PM, bharat gupta bharat.85.m...@gmail.comwrote: Sir, What about the description of replica_temp file that I posted in last mail. I think that's correct ... If you can comment on that, I can move on with replica_index file... On Thu, May 23, 2013 at 10:58 PM, Mark Abraham mark.j.abra...@gmail.com wrote: It's a demux. One might want trajectories to be at constant temperature, or constant replica. The two files define the (mutually inverse) mappings between those representations. So one file tells you which replica is at each temperature, and the other which temperature holds each replica. Nobody's ever written down anything about which is which, so like I said a week back, look at the first few exchanges, see how those are represented in the files, and decide for yourself which file's columns/rows have useful information you want to look at. And do write that decision down! :-) Mark On Thu, May 23, 2013 at 2:55 PM, simula_460 bharat.85.m...@gmail.com wrote: I checked the md.log and replica_temp.xvg file , what I understood is that the 'x' means swapping and replica are written this way. For eg. Replica exchange at step 1000 time 2 Repl 0 - 1 dE = -1.067e+00 Repl ex 0 x 123456789 10 11 12 x 13 Repl pr 1.0 .01 .68 .21 .05 .09 .26 output in replica_temp file will be 1 0 2 3 4 5 6 7 8 9 10 11 13 12 It means that replica 1 at higher temp. exchange with the one in lower temp 0. Replica exchange at step 2000 time 4 Repl ex 01 x 23456789 10 11 12 13 Repl pr.91 .32 .00 .07 .18 .08 output in replica_temp file will be 1 0 2 3 4 5 6 7 8 9 10 11 13 12 2 0 1 3 4 5 6 7 8 9 10 11 13 12 [order is from low to high temp] But I am not able to understand for replica_index file :- for the above two time steps here's the output :- 0 0123456789 10 11 12 13 2 1023456789 10 11 13 12 4 1203456789 10 11 13 12 The time step four is different here, I don't know why ?? Ideally the output should be same in both files, I suppose ?? Also, I tried to plot for each column separately , here I want to clarify that whether each column represents the time evolution of each replica over time. For eg. the second column should represent the temp evolution for replica No. 0 wrt to time. Presuming that I understood it correctly, I plotted the temp. evolution over time of all replicas separately . Here's the replica_temp plot for replicas 0 to 13. https://www.dropbox.com/s/0c8gp584v1hvlbx/replica_temp.png -- View this message in context: http://gromacs.5086.x6.nabble.com/REMD-analysis-tp5008199p5008481.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Re: REMD analysis
Dear Sir, My main objective of carrying out REMD is to study peptide folding and if possible to get some insight in protein design and folding. I read some articles related to my work and they always show temp (replica_index) graphs for 2-3 replicas , saying that the sufficient sampling had been achieved. In my case I checked the replica_temp for first three replicas ( https://www.dropbox.com/s/gkbu0g0e1r37l57/replica_temp0.png) ( https://www.dropbox.com/s/sffq8rwghjublu0/replica_temp1.png) https://www.dropbox.com/s/ulccw8xabj66ktm/replica_temp2.png) Almost all the three graphs are similar and the last 15ns shows that there is no enough exchange (if I have analyzed correctly) ?? In this case the acceptance ratio was fine and PE overlap was also good, but problem lies with efficient sampling ?? What shall I do in such a case ?? On Sat, May 18, 2013 at 12:27 AM, Mark Abraham mark.j.abra...@gmail.comwrote: On Fri, May 17, 2013 at 4:26 PM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, The the default bin width is 0.1 which I used for plotting the graphs. That's nice. You need to decide what you need to do about it if you want graphs that look like those you see reported :-) Another question is about your last reply to my thread exchange acceptance is a poor proxy for sampling efficiency. Sorry to ask this, but how to check whether the sampling efficiency is optimal or not (what should be optimal sampling efficiency) ?? Ah, now here's the real question :-) Spacing the replicas for optimal *flow* is a difficult problem, even for toy peptides, see e.g. papers by Nadler and Hansmann. Merely accepting exchanges does not imply flow. The belief is that getting flow enhances sampling, but the latter is hard to demonstrate without showing that simulation time to converged sampling actually reduces. I'm not aware of anybody who's actually done that - but it would certainly be an advantage if your application is interested in data at a range of temperatures. Mark On Fri, May 17, 2013 at 11:10 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Histograms 101: The smaller your bin width, the more variations you see. The more samples you have, the fewer variations you see. A histogram that does not mention either of this is a work of fiction. The number of degrees of freedom in the potential energy distribution is also a factor in whether the distribution will look smooth for a given bin width and number of samples. Mark On Fri, May 17, 2013 at 3:51 PM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, I tried plotting the PE overlap using the following way :- 1. extract PE of each replica using g_energy 2. get the PE distribution using g_analyze -f potential_0.xvg -dist pot0.xvg 3. used xmgrace to plot all the PE distribution graphs together. The same thing I did for temperature distribution for each replica. Here's the file for both PE overlap ( https://www.dropbox.com/s/895f1bi0hkuy884/pe_dist.png) temp distribution ( https://www.dropbox.com/s/ed66uop16blgqwa/temp_dist.png ) Is this the correct way ?? But the plot doesnot look like this ( https://www.dropbox.com/s/fsuabkl7zrydnib/sample%20PE%20overlap.jpg ). Do i have to normalize the data and then plot in order to get a smooth plot like this one?? Bharat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the
Re: [gmx-users] Re: REMD analysis
On Sat, May 18, 2013 at 5:17 PM, bharat gupta bharat.85.m...@gmail.comwrote: Dear Sir, My main objective of carrying out REMD is to study peptide folding and if possible to get some insight in protein design and folding. I read some articles related to my work and they always show temp (replica_index) graphs for 2-3 replicas , saying that the sufficient sampling had been achieved. In my case I checked the replica_temp for first three replicas ( https://www.dropbox.com/s/gkbu0g0e1r37l57/replica_temp0.png) ( https://www.dropbox.com/s/sffq8rwghjublu0/replica_temp1.png) https://www.dropbox.com/s/ulccw8xabj66ktm/replica_temp2.png) You've shown the same graph three times. Almost all the three graphs are similar and the last 15ns shows that there is no enough exchange (if I have analyzed correctly) ?? In this case the acceptance ratio was fine and PE overlap was also good, but problem lies with efficient sampling ?? Like I've been saying, acceptance does not assure enhanced sampling. What shall I do in such a case ?? Do some of the reading I've been suggesting? One of the papers shows that it is hard to get good sampling with just Met-enkephalin unless you design the temperature range for it. Mark On Sat, May 18, 2013 at 12:27 AM, Mark Abraham mark.j.abra...@gmail.com wrote: On Fri, May 17, 2013 at 4:26 PM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, The the default bin width is 0.1 which I used for plotting the graphs. That's nice. You need to decide what you need to do about it if you want graphs that look like those you see reported :-) Another question is about your last reply to my thread exchange acceptance is a poor proxy for sampling efficiency. Sorry to ask this, but how to check whether the sampling efficiency is optimal or not (what should be optimal sampling efficiency) ?? Ah, now here's the real question :-) Spacing the replicas for optimal *flow* is a difficult problem, even for toy peptides, see e.g. papers by Nadler and Hansmann. Merely accepting exchanges does not imply flow. The belief is that getting flow enhances sampling, but the latter is hard to demonstrate without showing that simulation time to converged sampling actually reduces. I'm not aware of anybody who's actually done that - but it would certainly be an advantage if your application is interested in data at a range of temperatures. Mark On Fri, May 17, 2013 at 11:10 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Histograms 101: The smaller your bin width, the more variations you see. The more samples you have, the fewer variations you see. A histogram that does not mention either of this is a work of fiction. The number of degrees of freedom in the potential energy distribution is also a factor in whether the distribution will look smooth for a given bin width and number of samples. Mark On Fri, May 17, 2013 at 3:51 PM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, I tried plotting the PE overlap using the following way :- 1. extract PE of each replica using g_energy 2. get the PE distribution using g_analyze -f potential_0.xvg -dist pot0.xvg 3. used xmgrace to plot all the PE distribution graphs together. The same thing I did for temperature distribution for each replica. Here's the file for both PE overlap ( https://www.dropbox.com/s/895f1bi0hkuy884/pe_dist.png) temp distribution ( https://www.dropbox.com/s/ed66uop16blgqwa/temp_dist.png ) Is this the correct way ?? But the plot doesnot look like this ( https://www.dropbox.com/s/fsuabkl7zrydnib/sample%20PE%20overlap.jpg ). Do i have to normalize the data and then plot in order to get a smooth plot like this one?? Bharat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at
Re: [gmx-users] Re: REMD analysis
Well use a regular plotting software and look at it or do some more elaborated operation in or out the software to estimate the overlap :)) On May 17, 2013, at 1:14 PM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, I ran the REMD simulation with temp. distribution discussed in my last thread. Each replica was run for 50 ns Replica exchange statistics Repl 24999 attempts, 12500 odd, 12499 even Repl average probabilities: Repl 0123456789 10 11 12 Repl .22 .19 .18 .16 .19 .21 .23 .25 .26 .29 .28 .28 Repl number of exchanges: Repl 0123456789 10 11 12 Repl 2661 2369 2296 2008 2360 2668 2866 3119 3234 3549 3469 3475 Repl average number of exchanges: Repl 0123456789 10 11 12 Repl .21 .19 .18 .16 .19 .21 .23 .25 .26 .28 .28 .28 Now, how to find the potential energy overlap for each replica??.. I have obtained the pot. energy for each replica separately.. -- Bharat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Re: REMD analysis
What do you not like in your distributions? What are your looking for in these distributions? I am not sure what you are expecting from the list here … your distributions are fine, but, as Mark noted, it does not mean your simulation and sampling will be optimal … On May 17, 2013, at 3:51 PM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, I tried plotting the PE overlap using the following way :- 1. extract PE of each replica using g_energy 2. get the PE distribution using g_analyze -f potential_0.xvg -dist pot0.xvg 3. used xmgrace to plot all the PE distribution graphs together. The same thing I did for temperature distribution for each replica. Here's the file for both PE overlap ( https://www.dropbox.com/s/895f1bi0hkuy884/pe_dist.png) temp distribution (https://www.dropbox.com/s/ed66uop16blgqwa/temp_dist.png) Is this the correct way ?? But the plot doesnot look like this ( https://www.dropbox.com/s/fsuabkl7zrydnib/sample%20PE%20overlap.jpg). Do i have to normalize the data and then plot in order to get a smooth plot like this one?? Bharat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Re: REMD analysis
Histograms 101: The smaller your bin width, the more variations you see. The more samples you have, the fewer variations you see. A histogram that does not mention either of this is a work of fiction. The number of degrees of freedom in the potential energy distribution is also a factor in whether the distribution will look smooth for a given bin width and number of samples. Mark On Fri, May 17, 2013 at 3:51 PM, bharat gupta bharat.85.m...@gmail.comwrote: Dear Sir, I tried plotting the PE overlap using the following way :- 1. extract PE of each replica using g_energy 2. get the PE distribution using g_analyze -f potential_0.xvg -dist pot0.xvg 3. used xmgrace to plot all the PE distribution graphs together. The same thing I did for temperature distribution for each replica. Here's the file for both PE overlap ( https://www.dropbox.com/s/895f1bi0hkuy884/pe_dist.png) temp distribution (https://www.dropbox.com/s/ed66uop16blgqwa/temp_dist.png ) Is this the correct way ?? But the plot doesnot look like this ( https://www.dropbox.com/s/fsuabkl7zrydnib/sample%20PE%20overlap.jpg). Do i have to normalize the data and then plot in order to get a smooth plot like this one?? Bharat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Re: REMD analysis
Dear Sir, The the default bin width is 0.1 which I used for plotting the graphs. Another question is about your last reply to my thread exchange acceptance is a poor proxy for sampling efficiency. Sorry to ask this, but how to check whether the sampling efficiency is optimal or not (what should be optimal sampling efficiency) ?? On Fri, May 17, 2013 at 11:10 PM, Mark Abraham mark.j.abra...@gmail.comwrote: Histograms 101: The smaller your bin width, the more variations you see. The more samples you have, the fewer variations you see. A histogram that does not mention either of this is a work of fiction. The number of degrees of freedom in the potential energy distribution is also a factor in whether the distribution will look smooth for a given bin width and number of samples. Mark On Fri, May 17, 2013 at 3:51 PM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, I tried plotting the PE overlap using the following way :- 1. extract PE of each replica using g_energy 2. get the PE distribution using g_analyze -f potential_0.xvg -dist pot0.xvg 3. used xmgrace to plot all the PE distribution graphs together. The same thing I did for temperature distribution for each replica. Here's the file for both PE overlap ( https://www.dropbox.com/s/895f1bi0hkuy884/pe_dist.png) temp distribution ( https://www.dropbox.com/s/ed66uop16blgqwa/temp_dist.png ) Is this the correct way ?? But the plot doesnot look like this ( https://www.dropbox.com/s/fsuabkl7zrydnib/sample%20PE%20overlap.jpg). Do i have to normalize the data and then plot in order to get a smooth plot like this one?? Bharat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Re: REMD analysis
On Fri, May 17, 2013 at 4:26 PM, bharat gupta bharat.85.m...@gmail.comwrote: Dear Sir, The the default bin width is 0.1 which I used for plotting the graphs. That's nice. You need to decide what you need to do about it if you want graphs that look like those you see reported :-) Another question is about your last reply to my thread exchange acceptance is a poor proxy for sampling efficiency. Sorry to ask this, but how to check whether the sampling efficiency is optimal or not (what should be optimal sampling efficiency) ?? Ah, now here's the real question :-) Spacing the replicas for optimal *flow* is a difficult problem, even for toy peptides, see e.g. papers by Nadler and Hansmann. Merely accepting exchanges does not imply flow. The belief is that getting flow enhances sampling, but the latter is hard to demonstrate without showing that simulation time to converged sampling actually reduces. I'm not aware of anybody who's actually done that - but it would certainly be an advantage if your application is interested in data at a range of temperatures. Mark On Fri, May 17, 2013 at 11:10 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Histograms 101: The smaller your bin width, the more variations you see. The more samples you have, the fewer variations you see. A histogram that does not mention either of this is a work of fiction. The number of degrees of freedom in the potential energy distribution is also a factor in whether the distribution will look smooth for a given bin width and number of samples. Mark On Fri, May 17, 2013 at 3:51 PM, bharat gupta bharat.85.m...@gmail.com wrote: Dear Sir, I tried plotting the PE overlap using the following way :- 1. extract PE of each replica using g_energy 2. get the PE distribution using g_analyze -f potential_0.xvg -dist pot0.xvg 3. used xmgrace to plot all the PE distribution graphs together. The same thing I did for temperature distribution for each replica. Here's the file for both PE overlap ( https://www.dropbox.com/s/895f1bi0hkuy884/pe_dist.png) temp distribution ( https://www.dropbox.com/s/ed66uop16blgqwa/temp_dist.png ) Is this the correct way ?? But the plot doesnot look like this ( https://www.dropbox.com/s/fsuabkl7zrydnib/sample%20PE%20overlap.jpg). Do i have to normalize the data and then plot in order to get a smooth plot like this one?? Bharat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
