Re: [gmx-users] adding metal ion
Adding an individual ion to a protein complex is simple: just open vmd or other visualization/building software, and position the ion where you expect it to be. Run energy minimization and check to make sure the ion is where you expect it to be. Now the tricky part is to make sure you have the proper parameters for the ion. With that in mind you should ask yourself, before going any further: Is the ion crucial to the behaviour of the system you are studying? If so, does the force-field you are using have the parameters for this ion? If not, you are going to need to find some. If no one has published any parameters, than you are going to need to parameterize the ion in question (selenium) yourself, which can be quite a labor intensive process. === Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Meenakshi Rajput ashi.rajpu...@gmail.com Sent: Monday, March 09, 2015 4:11 AM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] adding metal ion hello users I need to add selenium ion in the protein complex. Can anyone tell me how to add a metal ion in gromacs? I posted the question before but I didn't get any reply so I am posting again. Please tell me if anybody knows. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Error: see option -rdd, for pairs and tabulated bonds also see option -ddcheck
Hi All, I am doing CG membrane with protein. After running long simulation I am getting this error: Fatal error: 2 of the 13319 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (1.4 nm) or the two-body cut-off distance (1.4 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck For more information and tips for troubleshooting, please check the GROMACS I could not find this on google. Should I restart with something like -rdd 2 or so? I am just wondering how it will influence my overall calculations? I think it will reduce ns/day? or is there any serious energy related issues? Thanks, JIom -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Gromacs with InflateGro
Hi Anthony, I'm currently working on an alternative program to put things in an AA membrane. If you want, you can send me the protein (off-list) and I can give it a try. Cheers, Tsjerk On Sun, Mar 8, 2015 at 6:03 PM, Nash, Anthony a.n...@ucl.ac.uk wrote: Hi all, I'm really struggling to get InflateGro to work in a dimer + lipid (no water or ions) system. The fault seems to happen when the regular expression to break the .gro entry reads in an entry from C to C1. I managed to generalise the regex further and now using substr to explicitly pull out the entries I want. Unfortunately I'm a little confused as to the purpose of a variable called 'now'. Has anyone got a bullet proof copy of the code working with + atoms as I've had enough going through this file. I also tried InflateGro2, which passes the first two iterations but then dies after the second. It can't find tmp_out.gro, as the previous entry hadn't successfully passed grompp due to a difference in atom count between .gro and .top. Thanks Anthony -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Tsjerk A. Wassenaar, Ph.D. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 131, Issue 41
Hi Mark, -cl only gives me the central structure of that cluster. What I need is an expanded .xtc file with every structure in that cluster. Is there any way to realize that? Thank you, Xingcheng On Mon, Mar 9, 2015 at 6:00 AM, gromacs.org_gmx-users-requ...@maillist.sys.kth.se wrote: Send gromacs.org_gmx-users mailing list submissions to gromacs.org_gmx-users@maillist.sys.kth.se To subscribe or unsubscribe via the World Wide Web, visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or, via email, send a message with subject or body 'help' to gromacs.org_gmx-users-requ...@maillist.sys.kth.se You can reach the person managing the list at gromacs.org_gmx-users-ow...@maillist.sys.kth.se When replying, please edit your Subject line so it is more specific than Re: Contents of gromacs.org_gmx-users digest... Today's Topics: 1. Re: Separate .xtc file according to the result from g_cluster (Mark Abraham) 2. definition of eigenvector in gromacs (Brett) 3. adding metal ion (Meenakshi Rajput) 4. Re: definition of eigenvector in gromacs (Tsjerk Wassenaar) 5. Re: definition of eigenvector in gromacs (ms) -- Message: 1 Date: Mon, 9 Mar 2015 02:04:47 +0100 From: Mark Abraham mark.j.abra...@gmail.com To: Discussion list for GROMACS users gmx-us...@gromacs.org Subject: Re: [gmx-users] Separate .xtc file according to the result fromg_cluster Message-ID: camnumatwzvnrpfbjyeb3jdx6wjbt_szft2jmgq7o-4kzeke...@mail.gmail.com Content-Type: text/plain; charset=UTF-8 Hi, gmx cluster -h is a good friend ;-) see the -cl option. Mark On Mon, Mar 9, 2015 at 1:49 AM, Xingcheng Lin linxingcheng50...@gmail.com wrote: Hi, Is there any short way to seperate the .xtc file according to the results from g_cluster? For example, I want to chop the .xtc file into several small trajectories, each includes all the snapshots from the clusters given by g_cluster? Thank you, -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Message: 2 Date: Mon, 9 Mar 2015 09:33:16 +0800 (CST) From: Brett brettliu...@163.com To: gmx-users gmx-us...@gromacs.org Subject: [gmx-users] definition of eigenvector in gromacs Message-ID: 77570a06.253b.14bfc2a2adc.coremail.brettliu...@163.com Content-Type: text/plain; charset=GBK Dear All, Recently I have read a gromacs related article which contain a sentence Trajectories pojected on the first two eigenvectors. Will you please tell me the meaning of eigenvector and Trajectories pojected on the first two eigenvectors? Will you please also explain it to me using common-used words simple as desk, meal, earth, etc? Brett -- Message: 3 Date: Mon, 9 Mar 2015 13:41:01 +0530 From: Meenakshi Rajput ashi.rajpu...@gmail.com To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] adding metal ion Message-ID: cah5gtbke-72ayboctzh91jdq5z0_ew8nhmgbgmrvxzy6aug...@mail.gmail.com Content-Type: text/plain; charset=UTF-8 hello users I need to add selenium ion in the protein complex. Can anyone tell me how to add a metal ion in gromacs? I posted the question before but I didn't get any reply so I am posting again. Please tell me if anybody knows. -- Message: 4 Date: Mon, 9 Mar 2015 10:19:21 +0100 From: Tsjerk Wassenaar tsje...@gmail.com To: Discussion list for GROMACS users gmx-us...@gromacs.org Subject: Re: [gmx-users] definition of eigenvector in gromacs Message-ID: cabze1sjzo4e+6omb8_t_h3htvhjpr3m7wnpyvjczne+gmfk...@mail.gmail.com Content-Type: text/plain; charset=UTF-8 Hi Brett, Let's say you're sitting at your _desk_ writing that paper with a deadline yesterday and you put a quick _meal_ next to you, wondering why on _earth_ you keep up with this. Your hands are moving between the meal and the keyboard. You notice that the average position of your hands is somewhere between the two and mark the mean position on your desk. Then you draw a line through it that corresponds to the major extent of the motion of your hands, and write 'eigenvector 1' along it. You add a line through the average position, perfectly perpendicular to the first, and write 'eigenvector 2' along it. Now you can project every position of your hands onto your desk, giving it an 'eigenvector 1' coordinate (or score) and an 'eigenvector 2' coordinate (or score). You notice that it's only part of the total motion, as you neglect the height,
[gmx-users] Walls - segmentation fault
Hello, When I use walls with pbc =xy for the nanotube membrane - water system I get the following error which results in a segmentation fault: DD cell 0 0 0 could only obtain 126 of the 130 atoms that are connected via constraints from the neighboring cells. This probably means your constraint lengths are too long compared to the domain decomposition cell size. Decrease the number of domain decomposition grid cells or lincs-order. I have tried decreasing lincs order with no success.I am using Gromacs 4.6.1 (single precision), 2 cores. The simulation runs fine in 3d pbc without walls. Any suggestion would be greatly appreciated. Best regards, Michelle? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] walls - segmentation fault
Hello, When I use walls with pbc =xy for the nanotube membrane - water system I get the following error which results in a segmentation fault: DD cell 0 0 0 could only obtain 126 of the 130 atoms that are connected via constraints from the neighboring cells. This probably means your constraint lengths are too long compared to the domain decomposition cell size. Decrease the number of domain decomposition grid cells or lincs-order. I have tried decreasing lincs order with no success.I am using Gromacs 4.6.1 (single precision), 2 cores. The simulation runs fine in 3d pbc without walls. Any suggestion would be greatly appreciated. Best regards, Michelle?? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] definition of eigenvector in gromacs
lulz, that's gold! Now, is that too long for an end-of-mdrun GROMACS quote? :-) Mark On Mon, Mar 9, 2015 at 10:19 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Brett, Let's say you're sitting at your _desk_ writing that paper with a deadline yesterday and you put a quick _meal_ next to you, wondering why on _earth_ you keep up with this. Your hands are moving between the meal and the keyboard. You notice that the average position of your hands is somewhere between the two and mark the mean position on your desk. Then you draw a line through it that corresponds to the major extent of the motion of your hands, and write 'eigenvector 1' along it. You add a line through the average position, perfectly perpendicular to the first, and write 'eigenvector 2' along it. Now you can project every position of your hands onto your desk, giving it an 'eigenvector 1' coordinate (or score) and an 'eigenvector 2' coordinate (or score). You notice that it's only part of the total motion, as you neglect the height, which will be a third line, perpendicular to the desk. You can look at it a bit differently and say that your desk is the subspace of your real space, spanned by the two perpendicular vectors, which together describe most of your hand's motion. I hope this makes some sense :) Cheers, Tsjerk On Mon, Mar 9, 2015 at 2:33 AM, Brett brettliu...@163.com wrote: Dear All, Recently I have read a gromacs related article which contain a sentence Trajectories pojected on the first two eigenvectors. Will you please tell me the meaning of eigenvector and Trajectories pojected on the first two eigenvectors? Will you please also explain it to me using common-used words simple as desk, meal, earth, etc? Brett -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Tsjerk A. Wassenaar, Ph.D. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Error: see option -rdd, for pairs and tabulated bonds also see option -ddcheck
Hi, Very likely your run is blowing up from (long-time) instability - two atoms have moved some crazy amount. You can probably confirm that from the time series of some observables. Mark On Mon, Mar 9, 2015 at 12:54 PM, gromacs query gromacsqu...@gmail.com wrote: Hi All, I am doing CG membrane with protein. After running long simulation I am getting this error: Fatal error: 2 of the 13319 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (1.4 nm) or the two-body cut-off distance (1.4 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck For more information and tips for troubleshooting, please check the GROMACS I could not find this on google. Should I restart with something like -rdd 2 or so? I am just wondering how it will influence my overall calculations? I think it will reduce ns/day? or is there any serious energy related issues? Thanks, JIom -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 131, Issue 41
On Mon, Mar 9, 2015 at 4:33 PM, Xingcheng Lin linxingcheng50...@gmail.com wrote: Hi Mark, -cl only gives me the central structure of that cluster. What I need is an expanded .xtc file with every structure in that cluster. Is there any way to realize that? Yes, as documented in gmx cluster -h in the part that talks about -cl plus some other optional flags. :-) Mark Thank you, Xingcheng On Mon, Mar 9, 2015 at 6:00 AM, gromacs.org_gmx-users-requ...@maillist.sys.kth.se wrote: Send gromacs.org_gmx-users mailing list submissions to gromacs.org_gmx-users@maillist.sys.kth.se To subscribe or unsubscribe via the World Wide Web, visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or, via email, send a message with subject or body 'help' to gromacs.org_gmx-users-requ...@maillist.sys.kth.se You can reach the person managing the list at gromacs.org_gmx-users-ow...@maillist.sys.kth.se When replying, please edit your Subject line so it is more specific than Re: Contents of gromacs.org_gmx-users digest... Today's Topics: 1. Re: Separate .xtc file according to the result from g_cluster (Mark Abraham) 2. definition of eigenvector in gromacs (Brett) 3. adding metal ion (Meenakshi Rajput) 4. Re: definition of eigenvector in gromacs (Tsjerk Wassenaar) 5. Re: definition of eigenvector in gromacs (ms) -- Message: 1 Date: Mon, 9 Mar 2015 02:04:47 +0100 From: Mark Abraham mark.j.abra...@gmail.com To: Discussion list for GROMACS users gmx-us...@gromacs.org Subject: Re: [gmx-users] Separate .xtc file according to the result fromg_cluster Message-ID: camnumatwzvnrpfbjyeb3jdx6wjbt_szft2jmgq7o-4kzeke...@mail.gmail.com Content-Type: text/plain; charset=UTF-8 Hi, gmx cluster -h is a good friend ;-) see the -cl option. Mark On Mon, Mar 9, 2015 at 1:49 AM, Xingcheng Lin linxingcheng50...@gmail.com wrote: Hi, Is there any short way to seperate the .xtc file according to the results from g_cluster? For example, I want to chop the .xtc file into several small trajectories, each includes all the snapshots from the clusters given by g_cluster? Thank you, -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Message: 2 Date: Mon, 9 Mar 2015 09:33:16 +0800 (CST) From: Brett brettliu...@163.com To: gmx-users gmx-us...@gromacs.org Subject: [gmx-users] definition of eigenvector in gromacs Message-ID: 77570a06.253b.14bfc2a2adc.coremail.brettliu...@163.com Content-Type: text/plain; charset=GBK Dear All, Recently I have read a gromacs related article which contain a sentence Trajectories pojected on the first two eigenvectors. Will you please tell me the meaning of eigenvector and Trajectories pojected on the first two eigenvectors? Will you please also explain it to me using common-used words simple as desk, meal, earth, etc? Brett -- Message: 3 Date: Mon, 9 Mar 2015 13:41:01 +0530 From: Meenakshi Rajput ashi.rajpu...@gmail.com To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] adding metal ion Message-ID: cah5gtbke-72ayboctzh91jdq5z0_ew8nhmgbgmrvxzy6aug...@mail.gmail.com Content-Type: text/plain; charset=UTF-8 hello users I need to add selenium ion in the protein complex. Can anyone tell me how to add a metal ion in gromacs? I posted the question before but I didn't get any reply so I am posting again. Please tell me if anybody knows. -- Message: 4 Date: Mon, 9 Mar 2015 10:19:21 +0100 From: Tsjerk Wassenaar tsje...@gmail.com To: Discussion list for GROMACS users gmx-us...@gromacs.org Subject: Re: [gmx-users] definition of eigenvector in gromacs Message-ID: cabze1sjzo4e+6omb8_t_h3htvhjpr3m7wnpyvjczne+gmfk...@mail.gmail.com Content-Type: text/plain; charset=UTF-8 Hi Brett, Let's say you're sitting at your _desk_ writing that paper with a deadline yesterday and you put a quick _meal_ next to you, wondering why on _earth_ you keep up with this. Your hands are moving between the meal and the keyboard. You notice that the average position of your hands is somewhere between the two and mark the mean position on your desk. Then you draw a line through it that corresponds to the major extent of the motion of your hands, and write 'eigenvector 1' along it. You add a line through
[gmx-users] initial position?
Hi, I have simulated ionomer on Pt surface. I freezed the Pt and put 5 ionomer polymers on top of it in a distance. Depends on the position of these polymers, it will get different results. Is it possible? For some cases, the ionomer backbone goes out of the box and interact with the neighbor molecules. How can I solve this problem? Kind regards, Ehsan Confidentiality Notice The information contained in this communication is confidential and/or proprietary business or technical data. It is intended for receipt only by the addressee listed above. If you are not the intended recipient, you are hereby notified that any dissemination, copying or distribution of this communication, or the taking of any action in reliance on the contents of this communication, is strictly prohibited. If you have received this communication in error, please immediately notify us electronically by return message, and delete or destroy all copies of this communication. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Writing out the neighbor list
Hi, Not really. gmx mdrun -debug n for sufficiently large n (3?) will print out the IDs of the i and j clusters that are in the cluster-pair list for its duration, but of course that's buffered and does not correspond directly to anything that leads to physics. To get a list of particles that interact at a given time step, you'd have to hack a C kernel that also dumped the atom indices of pairs that were actually within the cutoff; very doable for the single-domain case, but not already done for you. Mark On Mon, Mar 9, 2015 at 9:48 PM, Alan Manning mann...@physics.ubc.ca wrote: Hi Is it possible to have Gromacs write out the neighbor lists as well as the trajectories? Thanks. Regards, Alan Manning -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] initial position?
On 3/9/15 4:56 PM, Sadeghi, Ehsan wrote: Hi, I have simulated ionomer on Pt surface. I freezed the Pt and put 5 ionomer polymers on top of it in a distance. Depends on the position of these polymers, it will get different results. Is it possible? For some cases, the ionomer backbone goes out of the box and interact with the neighbor molecules. How can I solve this problem? This is why it is standard practice to run multiple simulations from different starting velocities or initial configurations. Proper sampling is key. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Writing out the neighbor list
Ah OK. I'll probably implement a neighbor list after the fact from the trajectory data itself. Thanks. On 15-03-09 03:17 PM, Mark Abraham wrote: Hi, Not really. gmx mdrun -debug n for sufficiently large n (3?) will print out the IDs of the i and j clusters that are in the cluster-pair list for its duration, but of course that's buffered and does not correspond directly to anything that leads to physics. To get a list of particles that interact at a given time step, you'd have to hack a C kernel that also dumped the atom indices of pairs that were actually within the cutoff; very doable for the single-domain case, but not already done for you. Mark On Mon, Mar 9, 2015 at 9:48 PM, Alan Manning mann...@physics.ubc.ca wrote: Hi Is it possible to have Gromacs write out the neighbor lists as well as the trajectories? Thanks. Regards, Alan Manning -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] definition of eigenvector in gromacs
Tsjerk, that's one of the coolest explanations of PCA I've ever read! :) Just one additional comment for Brett: Tsjerk's example assumes implicitly that your hands are actually moving parallel to the desk on average. On my desk, the meal is usually on top of the pile of papers that mysteriously keeps growing to the left of my keyboard. So, my hands don't move parallel to the desk, but along an inclined plane that raises from the keyboard to the meal position and is slightly tilted towards me (yeah, I know I should sit straight...). Therefore, the average position of my hands and their direction of major extent (eigenvector 1) should be marked on that plane, not on the desk, and the second direction (eigenvector 2) is a line also on that plane drawn perpendicularly to the first. As in Tsjerk's example, if I project every position of my hands onto this resulting PCA plane I will probably capture most of their motion, without having to consider the third direction perpendicular to the plane. My point is that the subspace obtained from PCA is often different from the one that seems more natural to us (which was perhaps not obvious in Tsjerk's example). Although my desk is the natural reference frame when I'm working, my hands' motion can be more easily described in terms of positions on the plane I've just described, since I roughly need just 2 coordinates instead of the original 3. That's the aim of PCA -- to describe the original motion using fewer coordinates. Incidentally, this also shows that a messy desk is scientifically more fruitful than a tidy one... ;) Cheers, Antonio On Mon, 9 Mar 2015, Tsjerk Wassenaar wrote: Hi Brett, Let's say you're sitting at your _desk_ writing that paper with a deadline yesterday and you put a quick _meal_ next to you, wondering why on _earth_ you keep up with this. Your hands are moving between the meal and the keyboard. You notice that the average position of your hands is somewhere between the two and mark the mean position on your desk. Then you draw a line through it that corresponds to the major extent of the motion of your hands, and write 'eigenvector 1' along it. You add a line through the average position, perfectly perpendicular to the first, and write 'eigenvector 2' along it. Now you can project every position of your hands onto your desk, giving it an 'eigenvector 1' coordinate (or score) and an 'eigenvector 2' coordinate (or score). You notice that it's only part of the total motion, as you neglect the height, which will be a third line, perpendicular to the desk. You can look at it a bit differently and say that your desk is the subspace of your real space, spanned by the two perpendicular vectors, which together describe most of your hand's motion. I hope this makes some sense :) Cheers, Tsjerk On Mon, Mar 9, 2015 at 2:33 AM, Brett brettliu...@163.com wrote: Dear All, Recently I have read a gromacs related article which contain a sentence Trajectories pojected on the first two eigenvectors. Will you please tell me the meaning of eigenvector and Trajectories pojected on the first two eigenvectors? Will you please also explain it to me using common-used words simple as desk, meal, earth, etc? Brett -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Tsjerk A. Wassenaar, Ph.D. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Antonio M. Baptista Instituto de Tecnologia Quimica e Biologica, Universidade Nova de Lisboa Av. da Republica - EAN, 2780-157 Oeiras, Portugal phone: +351-214469619 email: bapti...@itqb.unl.pt fax: +351-214411277 WWW: http://www.itqb.unl.pt/~baptista -- -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] definition of eigenvector in gromacs
Hi Brett, Let's say you're sitting at your _desk_ writing that paper with a deadline yesterday and you put a quick _meal_ next to you, wondering why on _earth_ you keep up with this. Your hands are moving between the meal and the keyboard. You notice that the average position of your hands is somewhere between the two and mark the mean position on your desk. Then you draw a line through it that corresponds to the major extent of the motion of your hands, and write 'eigenvector 1' along it. You add a line through the average position, perfectly perpendicular to the first, and write 'eigenvector 2' along it. Now you can project every position of your hands onto your desk, giving it an 'eigenvector 1' coordinate (or score) and an 'eigenvector 2' coordinate (or score). You notice that it's only part of the total motion, as you neglect the height, which will be a third line, perpendicular to the desk. You can look at it a bit differently and say that your desk is the subspace of your real space, spanned by the two perpendicular vectors, which together describe most of your hand's motion. I hope this makes some sense :) Cheers, Tsjerk On Mon, Mar 9, 2015 at 2:33 AM, Brett brettliu...@163.com wrote: Dear All, Recently I have read a gromacs related article which contain a sentence Trajectories pojected on the first two eigenvectors. Will you please tell me the meaning of eigenvector and Trajectories pojected on the first two eigenvectors? Will you please also explain it to me using common-used words simple as desk, meal, earth, etc? Brett -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Tsjerk A. Wassenaar, Ph.D. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] adding metal ion
hello users I need to add selenium ion in the protein complex. Can anyone tell me how to add a metal ion in gromacs? I posted the question before but I didn't get any reply so I am posting again. Please tell me if anybody knows. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] definition of eigenvector in gromacs
I am gluing this email exchange to my office wall. This is just awesome. Thanks to you all. On 3/9/15 10:19 AM, Tsjerk Wassenaar wrote: Hi Brett, Let's say you're sitting at your _desk_ writing that paper with a deadline yesterday and you put a quick _meal_ next to you, wondering why on _earth_ you keep up with this. Your hands are moving between the meal and the keyboard. You notice that the average position of your hands is somewhere between the two and mark the mean position on your desk. Then you draw a line through it that corresponds to the major extent of the motion of your hands, and write 'eigenvector 1' along it. You add a line through the average position, perfectly perpendicular to the first, and write 'eigenvector 2' along it. Now you can project every position of your hands onto your desk, giving it an 'eigenvector 1' coordinate (or score) and an 'eigenvector 2' coordinate (or score). You notice that it's only part of the total motion, as you neglect the height, which will be a third line, perpendicular to the desk. You can look at it a bit differently and say that your desk is the subspace of your real space, spanned by the two perpendicular vectors, which together describe most of your hand's motion. I hope this makes some sense :) Cheers, Tsjerk On Mon, Mar 9, 2015 at 2:33 AM, Brett brettliu...@163.com wrote: Dear All, Recently I have read a gromacs related article which contain a sentence Trajectories pojected on the first two eigenvectors. Will you please tell me the meaning of eigenvector and Trajectories pojected on the first two eigenvectors? Will you please also explain it to me using common-used words simple as desk, meal, earth, etc? Brett -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
