[gmx-users] How to visualize .edo file
Hi All, I have generated a .edo file through mdrun and now want to analyze it. Can anyone tell me how to visualize/analyze this .edo file. All suggestions are welcome. Regards, Anirban Ghosh M.Tech Bioinformatics University of Hyderabad Hyderabad - 500 046 Andhra Pradesh India - Get the freedom to save as many mails as you wish. Click here to know how.___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Atomic distances problems using gmxcheck
yudaqi wrote: Hello gmx-users: When using gmxcheck to compare the bond length in .tpr files and .trr files, I get the following long list error: Distance between atoms 1 and 2 is 0.100, should be 0.010 Distance between atoms 1 and 3 is 0.101, should be 0.010 Distance between atoms 1 and 4 is 0.100, should be 0.010 Distance between atoms 1 and 5 is 0.146, should be 0.022 If you look close the expected distance seems to be the square of the distance. Could it be you are using a GROMOS force field? .. I have searched the maillists in the web site of gromacs, and found the same problems has been issued by other users. However, I can not find detailed explanations about this. So I wonder why the bond length should be of the order of 0.01 nm? Thank you very much. YuDaqi ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Atomic distances problems using gmxcheck
yudaqi wrote: Hello gmx-users: When using gmxcheck to compare the bond length in .tpr files and .trr files, I get the following long list error: Distance between atoms 1 and 2 is 0.100, should be 0.010 Distance between atoms 1 and 3 is 0.101, should be 0.010 Distance between atoms 1 and 4 is 0.100, should be 0.010 Distance between atoms 1 and 5 is 0.146, should be 0.022 .. I have searched the maillists in the web site of gromacs, and found the same problems has been issued by other users. However, I can not find detailed explanations about this. So I wonder why the bond length should be of the order of 0.01 nm? I fixed it in CVS. Will be in 3.3.2 Thank you very much. YuDaqi ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Mmxcheck Messages and Timesteps
Hello Gromacs users, I ran gmxcheck on a trr file I got from running energy minimization, Gmxcheck's output is: - Checking file 4PLMYWOrg01_em_tim.trr trn version: GMX_trn_file (single precision) Reading frame 0 time0.000 # Atoms 55986 Reading frame 11 time 1001.000 Timesteps at t=1000 don't match (100, 1) Last frame 11 time 1001.000 Item#frames Step12 Time12 Lambda 12 Coords 11 Velocities 0 Forces 1 Box 12 gcq#259: Everything Must Go (Red Hot Chili Peppers) -- So my question is - What does that mean Timesteps at t=1000 don't match..? (and where can I find more information regarding to gmxcheck messages?) Thank you in advance, Shay Amram ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Mmxcheck Messages and Timesteps
Shay Amram wrote: Hello Gromacs users, I ran gmxcheck on a trr file I got from running energy minimization, Gmxcheck’s output is: - */ Checking file 4PLMYWOrg01_em_tim.trr /* */ trn version: GMX_trn_file (single precision) /* */ Reading /* */ frame 0 time0.000 /* */ # Atoms 55986 /* */ Reading frame 11 time 1001.000 /* */ Timesteps at t=1000 don't match (100, 1) /* */ Last frame 11 time 1001.000 /* */ /* */ /* */ Item#frames /* */ Step12 /* */ Time12 /* */ Lambda 12 /* */ Coords 11 /* */ Velocities 0 /* */ Forces 1 /* */ Box /* */ 12 /* */ /* */ /* */ gcq#259: Everything Must Go (Red Hot Chili Peppers) /* -- So my question is – What does that mean “Timesteps at t=1000 don’t match….”? (and where can I find more information regarding to gmxcheck messages?) nowehere I'm afraid. These messages are intended for MD trajectories in which case you usually want to have the same time step between frames. For EM this is meaningless. Thank you in advance, Shay Amram ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] RE: Neutralising charge distribution
Hi Jeroen Thank you for your reply. I just wanted to know whether the correction term for the 'uniform background charge' is included in the code; I didn't meant to to take it out. Another thing is about the dipole correction that is applied for conducting boundary conditions. Is it switched off in PME when epsilon-surface is 0? Regards George -Original Message- From: [EMAIL PROTECTED] on behalf of van Bemmelen Sent: Tue 9/18/2007 11:14 AM To: gmx-users@gromacs.org Subject: [gmx-users] RE: Neutralising charge distribution Hi George, Yes, such a correction term exists, but it's a divergent term. This term is IMPLICITLY included in the energy, since it compensates for the divergent part in the reciprocal space term, leaving a constant term. This constant term is included explicitly in the code. You could take this constant term out. But be very aware that this constant term not only represents the 'uniform background charge' (or 'neutralising charge distribution', if you will) but also the divergent part of reciprocal space term. So simply leaving it out would be highly unphysical, at least in my opinion. If you really want to know more, I suggest digging into the formulas yourself. :-) Greetz, Jeroen Date: Mon, 17 Sep 2007 16:17:17 +0100 From: Georgios Patargias [EMAIL PROTECTED] Subject: [gmx-users] Neutralising charge distribution To: gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=iso-8859-1 Hello I would like to ask what is the functional form of the uniform neutralising charge distribution applied in Gromacs when doing PME on a charged system. Is there a correction term for this charge distribution that is included in the calculation of energies? Thanks George ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php winmail.dat___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] RE: Neutralising charge distribution
Georgios Patargias wrote: Hi Jeroen Thank you for your reply. I just wanted to know whether the correction term for the 'uniform background charge' is included in the code; I didn't meant to to take it out. Another thing is about the dipole correction that is applied for conducting boundary conditions. Is it switched off in PME when epsilon-surface is 0? check the equations in the manual, they are correct (famous last words...) Regards George -Original Message- From: [EMAIL PROTECTED] on behalf of van Bemmelen Sent: Tue 9/18/2007 11:14 AM To: gmx-users@gromacs.org Subject: [gmx-users] RE: Neutralising charge distribution Hi George, Yes, such a correction term exists, but it's a divergent term. This term is IMPLICITLY included in the energy, since it compensates for the divergent part in the reciprocal space term, leaving a constant term. This constant term is included explicitly in the code. You could take this constant term out. But be very aware that this constant term not only represents the 'uniform background charge' (or 'neutralising charge distribution', if you will) but also the divergent part of reciprocal space term. So simply leaving it out would be highly unphysical, at least in my opinion. If you really want to know more, I suggest digging into the formulas yourself. :-) Greetz, Jeroen Date: Mon, 17 Sep 2007 16:17:17 +0100 From: Georgios Patargias [EMAIL PROTECTED] Subject: [gmx-users] Neutralising charge distribution To: gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=iso-8859-1 Hello I would like to ask what is the functional form of the uniform neutralising charge distribution applied in Gromacs when doing PME on a charged system. Is there a correction term for this charge distribution that is included in the calculation of energies? Thanks George ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] RE: Neutralising charge distribution
Hi George, Sorry, I got a bit carried away. Actually, I once thought of somehow taking it out myself, so probably that's why. ;-) About the dipole correction: I haven't experimented with it myself, but I'm pretty sure it's switched off when epsilon_surface is 0. That's also what the manual says (see http://www.gromacs.org/documentation/reference/online/mdp_opt.html#ewald ): The default value of zero means it is turned off. If you need to be certain about what's exactly going on in the code, you may want to check the function ewald_LRcorrection in the file ewald_util.c. Hope it helps, Jeroen Date: Wed, 19 Sep 2007 10:40:52 +0100 From: Georgios Patargias [EMAIL PROTECTED] Subject: RE: [gmx-users] RE: Neutralising charge distribution To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=iso-8859-1 Hi Jeroen Thank you for your reply. I just wanted to know whether the correction term for the 'uniform background charge' is included in the code; I didn't meant to to take it out. Another thing is about the dipole correction that is applied for conducting boundary conditions. Is it switched off in PME when epsilon-surface is 0? Regards George ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] RE: Neutralising charge distribution
Hi Jeroen Thanks once again for your reply. Best wishes George -Original Message- From: [EMAIL PROTECTED] on behalf of van Bemmelen Sent: Wed 9/19/2007 11:16 AM To: gmx-users@gromacs.org Subject: [gmx-users] RE: Neutralising charge distribution Hi George, Sorry, I got a bit carried away. Actually, I once thought of somehow taking it out myself, so probably that's why. ;-) About the dipole correction: I haven't experimented with it myself, but I'm pretty sure it's switched off when epsilon_surface is 0. That's also what the manual says (see http://www.gromacs.org/documentation/reference/online/mdp_opt.html#ewald ): The default value of zero means it is turned off. If you need to be certain about what's exactly going on in the code, you may want to check the function ewald_LRcorrection in the file ewald_util.c. Hope it helps, Jeroen Date: Wed, 19 Sep 2007 10:40:52 +0100 From: Georgios Patargias [EMAIL PROTECTED] Subject: RE: [gmx-users] RE: Neutralising charge distribution To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=iso-8859-1 Hi Jeroen Thank you for your reply. I just wanted to know whether the correction term for the 'uniform background charge' is included in the code; I didn't meant to to take it out. Another thing is about the dipole correction that is applied for conducting boundary conditions. Is it switched off in PME when epsilon-surface is 0? Regards George ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php winmail.dat___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] topology of Alpha d-mannopyranosyl (1-6) alpha d-mannopyranose
parichita parichita wrote: Thaks for your suggesion... I want to use Gromacs for MD on my disaccharides in explicit water box.Now, the problem I encounter is that the pdb2gmx produces the topologies where hydrogens sitting on carbons are condensed on carbon atoms they sit on. I need them explicitly since I would like to study the NMR coupling contanst of hydroxy protons and C-H protons.I mean 3J(H-O-C-H) and measure the distance between the C-H proton through the glycosidic linkage. So my questions are; 1- Are the force fields(45a3,53a5) that are implemented in Gromacs capable of taking care of hydrogens sitting on carbon atoms in a sugar molecule explicitly? See below, and http://wiki.gromacs.org/index.php/Force_Fields 2- How can I most reliably produce topologies for my disaccharide that will be placed in a water box to perform MD? pdb2gmx... you should find and do some tutorial material to learn about this. I am quite new to MD methods therefore I apologize already now if I put forward something incoherent. You should definitely be doing some background reading of textbooks and tutorials if you haven't yet come across the phenomena of united-atom and all-atom force fields. MD simulations are fabulously easy ways to generate very expensive random numbers, and there's no substitute for library work and careful experimentation. The first few chapters of the GROMACS manual are a good place to start. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] topology of Alpha d-mannopyranosyl (1-6) alpha d-mannopyranose
Thaks for your suggesion... I want to use Gromacs for MD on my disaccharides in explicit water box.Now, the problem I encounter is that the pdb2gmx produces the topologies where hydrogens sitting on carbons are condensed on carbon atoms they sit on. I need them explicitly since I would like to study the NMR coupling contanst of hydroxy protons and C-H protons.I mean 3J(H-O-C-H) and measure the distance between the C-H proton through the glycosidic linkage. So my questions are; 1- Are the force fields(45a3,53a5) that are implemented in Gromacs capable of taking care of hydrogens sitting on carbon atoms in a sugar molecule explicitly? 2- How can I most reliably produce topologies for my disaccharide that will be placed in a water box to perform MD? I am quite new to MD methods therefore I apologize already now if I put forward something incoherent. Thanks for the help, Tsjerk Wassenaar [EMAIL PROTECTED] wrote: Parichita, My guess is you only thought to have 1-6 linkage, because the atoms seemed so nicely involved in the .pdb file. But you'll have to define a bond explicitly or it won't be there to break in the first place. I think you need to read up on topologies, force fields and general background about simulating molecular systems. Chapter 5 is a must. If you continue on this path, note that sugar dihedrals, especially the ones connecting the rings, are complex. Check out Roberto Lins' paper on the 45a3 force field. Tsjerk On 9/17/07, Mark Abraham wrote: parichita parichita wrote: Hi again. Thank you for your help I found my MANA in the ffG53a5.rtp and i can prepare the .gro and .top file from pdb2gmx. Now , i am facing another problem after solvation of my solute when i run the minimization the 1-6 linkage was broken .. please help me out linkage was broken doesn't help us help you. Please describe in detail what you observed and why you think it was wrong. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Parichita Mazumder Junior Research Fellow C/O Dr. Chaitali Mukhopadhayay Department of Chemistry University of Calcutta 92,A P C Road Kolkata-79 India. - Save all your chat conversations. Find them online.___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] MD simulation of Alpha d-mannopyranosyl (1-6) alpha d-mannopyranose
Hi Somer, I want to simulate my Alpha d-mannopyranosyl (1-6) alpha d-mannopyranose explicitly using my NOE restrain. I am new to MD using GROMACS . Please,give some thought . Thanks in advance parichita Parichita Mazumder Junior Research Fellow C/O Dr. Chaitali Mukhopadhayay Department of Chemistry University of Calcutta 92,A P C Road Kolkata-79 India. - Save all your chat conversations. Find them online.___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] RE: Neutralising charge distribution
Actually, I'd say they're not incorrect, but incomplete (well, for many systems). There's no mention of the correction terms George was asking about, only the self correction term is taken into account in those equations. But they're in the code allright, and a lot can be induced from the mdp parameters. Jeroen check the equations in the manual, they are correct (famous last words...) David van der Spoel, Ph.D. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] POPC simulation
thanks for reply.I want to perform simulation of popc membrane. Steps which i have done are as follows: 1. download popc128a.pdb, popc.it,lipids.itp (http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies) 2. download ffgmx_lipids files 3.convert POPC of .top popc.itp into POP as in popc.gro 4. #include ffgmx.itp #include lipid.itp #include popc.itp #include ffgmxnb.itp #include ffgmxbon.itp in my .top file. Now when I perform pdb2gmx -ff gmx -f popc128a.pdb -o popc.gro -p popc.top it shows the error thatResidue 'POP' not found in residue topology database. I think that's because of the fact that ffgmx.rtp do not contain POP residue ,but it has DPPC residue. Plz suggest how can i solve this problem. thanks. - Meet people who discuss and share your passions. Join them now.___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] POPC simulation
Quoting Moutusi Manna [EMAIL PROTECTED]:
thanks for reply.I want to perform simulation of popc membrane.
Steps which i have done are as follows:
1. download popc128a.pdb, popc.it,lipids.itp
(http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies)
2. download ffgmx_lipids files
3.convert POPC of .top popc.itp into POP as in popc.gro
4. #include ffgmx.itp
#include lipid.itp
#include popc.itp
#include ffgmxnb.itp
#include ffgmxbon.itp
These last two lines should already be included in ffgmx.itp, and including them
twice may cause some headaches.
in my .top file.
Now when I perform
pdb2gmx -ff gmx -f popc128a.pdb -o popc.gro -p popc.top
it shows the error thatResidue 'POP' not found in residue topology
database.
I think that's because of the fact that ffgmx.rtp do not
contain POP residue ,but it has DPPC residue.
Plz suggest how can i solve this problem.
thanks.
Use editconf to convert between .pdb and .gro. You only need pdb2gmx if you
don't have a .top file, but Prof. Tieleman has kindly provided this for you
already, in the form of lipid.itp and popc.itp.
-Justin
==
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
[EMAIL PROTECTED] | (540) 231-9080
http://bevanlab.biochem.vt.edu/Pages/Personal/justin/
==
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Re: Re: [gmx-users] Atomic distances problems using gmxcheck
Hello David: Yes, you are right. the value equals to the square of the distance, approximately. In fact, the force field I used was GROMOS96 43a1 force field. I have also tried the other kind of force fields, such as OPLS-AA/L all-atom force field, the same warning was reported, but the should be value seemed much more reasonable. Thank you very much for your help! 在 2007-09-19三的 08:24 [EMAIL PROTECTED] Message: 5 Date: Wed, 19 Sep 2007 08:24:25 +0200 From: David van der Spoel [EMAIL PROTECTED] Subject: Re: [gmx-users] Atomic distances problems using gmxcheck To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1; format=flowed yudaqi wrote: Hello gmx-users: When using gmxcheck to compare the bond length in .tpr files and .trr files, I get the following long list error: Distance between atoms 1 and 2 is 0.100, should be 0.010 Distance between atoms 1 and 3 is 0.101, should be 0.010 Distance between atoms 1 and 4 is 0.100, should be 0.010 Distance between atoms 1 and 5 is 0.146, should be 0.022 If you look close the expected distance seems to be the square of the distance. Could it be you are using a GROMOS force field? .. I have searched the maillists in the web site of gromacs, and found the same problems has been issued by other users. However, I can not find detailed explanations about this. So I wonder why the bond length should be of the order of 0.01 nm? Thank you very much. YuDaqi ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Atomic distances problems using gmxcheck (David van der Spoel)
Hello, David I have download the CVS version 3.3.2. it works well. Thank you very much for your hard work in gromacs. YuDaqi 在 2007-09-19三的 11:45 [EMAIL PROTECTED] Re: Atomic distances problems using gmxcheck (David van der Spoel) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Impulsive motion resulting from AFM pulling
Hello everyone, Eventually I want to pull a carbon nanotube through water at a constant rate. Before I get to this, I'm pulling a nanotube in vacuum just to make sure I'm using the pull code correctly. My system consists of a carbon nanotube aligned along the z axis and a single dummy atom fixed on the z axis. Here is my pull.ppa file: runtype = afm ngroups = 1 group_1 = nanotube pulldim = Y N N reference_group = dummy reftype = com afm_rate1 = 0.1 afm_dir1 = 1 0 0 afm_k1 = 10 afm_init1 = 2.00 2.00 4.042 Here, the coordinates for afm_init1 is the initial center of mass of the nanotube (thus, the system should start out with zero applied force). Applying this pulling force results in the nanotube undergoing a complicated oscillation as it moves along the +x direction. A graph of the nanotube position as a function of time is shown here: http://dept.physics.upenn.edu/~robertjo/gmx/nt-position.jpg What is causing oscillations of this type? I was expecting the nanotube to move at a constant rate. Does this have anything to do with the fact that I'm pulling the nanotube in vacuum? Perhaps in aqueous solution, the solvent will damp these types of oscillations. Any ideas as to how to remove this? Thanks, Bob ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] VDW Default and PME question
Hi All, Does anyone know what the default vdw type if none is specified? Is the value in brackets in the manual the default? If so, there is none listed for VWD type. Additionally, if PME is selected as the coulombtype, do the cutoffs matter? I am a bit confused in this regard. Thanks in advance, Jason ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] AFM Pulling and com motion
Hi GXM Users, I'm trying to execute some AFM Pulling. I followed the pull code tutorial from GMX WORKSHOP 2007, and I found there is no specific to com motion in mdp, so the default is comm-mode=Linear and comm-grps=System. I was confused about it as I believed we should not stopcm when doing AFM Pulling because of the external force. Does it problematic to stopcm when doing AFM Pulling? Thanks! ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
