Re: [gmx-users] Cross-linking of polymers
Dear Dr. Warren: Thank you for your answer and sorry for my ignorantness. I will do more literature survey... Thank you again. Sincerely, Kim On Sun, Mar 22, 2009 at 11:30 PM, Dallas B. Warren dallas.war...@pharm.monash.edu.au wrote: Kim, Recently I have been focusing on cross-linking phenomenon of polymers. As far as I understood, cross-linking include bond breaks in one polymer chain and bond occurrences among broken chains. I guess OPLS-aa is not suitable for this purpose, and my question is this. Is my guess correct? OPLS-aa is for molecular dynamics, no bond breaking or formation can happen, so you cannot use it when you that happening. If so, what others can be used for this purpose? ReaxFF or RWFF? Appears so, http://en.wikipedia.org/wiki/Force_field_(chemistry)#Reactive_Force_Fiel ds You really need to do a literature search and see what others doing similar things are using etc. Additionally, should I combine those potentials (ReaxFF or RWFF) with OPLS-aa force fields to mimic cross-linking (comes from RWFF etc.) of a realistic polymers (comes from OPLS-aa)? Depends on the other forcefield and if it has been derived and is compatible with OPLS-aa. Read point 1 on this page http://wiki.gromacs.org/index.php/Parameterization Without having read about those forcefields, highly unlikely that you can mix them. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Cross-linking of polymers
Dear All: I appreciate your care and help all the time. As you may know I am trying to simulate polymer behaviors. Recently I have been focusing on cross-linking phenomenon of polymers. As far as I understood, cross-linking include bond breaks in one polymer chain and bond occurrences among broken chains. I guess OPLS-aa is not suitable for this purpose, and my question is this. Is my guess correct? If so, what others can be used for this purpose? ReaxFF or RWFF? Additionally, should I combine those potentials (ReaxFF or RWFF) with OPLS-aa force fields to mimic cross-linking (comes from RWFF etc.) of a realistic polymers (comes from OPLS-aa)? Thank you so much!! Sincerely, Kim ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Matching atom name and types in OPLS-aa FF
Dear Justin: Thank you for your email! Thanks to your help and explanation, I am feeling more comfortable with OPLS topology modification. Before this work, I have used Gromacs without modifying FF paramters for simulating 'water' in general systems, which can easily obtained from PDB sites. So, it was not too easy to generate a sort of new topology even I've learned MD. I understand what you meant here. :) I did not mean the selection 1 (Harmonic potential function) is a sort of OPLS-aa FF functions. My question is actually if I can use the Forth power potential when I choose 2 in bond streching section. Since this funtion has different from from 1 (Harmonic potential function), I thought that it may need other paramters that may (may not) be different from the given parameters in OPLS-aa FF. So, my question here is [can I use the Forth power potential for bond strech using the given OPLS-aa paramters?] I assume this would be same to others, angle, dihedral, and etc. Thank you again. Sincerely, Kim On Mon, 16 Mar 2009, Justin A. Lemkul wrote: Tree wrote: Dear Dr. Periole: Thank you for your answer. You meant that the types of potential functions do not have any relations with OPLS-aa (except first (1) case). Those (from 2...) are defined as written the Gromacs manual. Table 5.4 defines the different types of intramolecular interactions. You should specify the proper terms based on what corresponds to the force field functional form. That is harmonic potential does not necessarily imply OPLS, but OPLS might imply that you have to use a harmonic potential (because, in fact, many force fields use a harmonic potential for bonds, not just OPLS!) You should refer to the primary literature for the force field, how it was derived, and any subsequent references regarding modifications to the force field. Another option (in addition to doing the background reading!) is to run through some tutorial material with a simple protein under OPLS to get a feel for how an OPLS topology is automatically created by pdb2gmx. -Justin Thank you again. Sincerely, Kim On Mon, Mar 16, 2009 at 5:42 PM, XAvier Periole x.peri...@rug.nl mailto:x.peri...@rug.nl wrote: On Mar 16, 2009, at 9:34 AM, tree wrote: Dear Justin and All: I truly appreciate your clear answer. Since my questions are solved by your explanations, I do not know how I can express my grateful heart. Now I have to ask second step questions. :) It is related to the OPLS-aa bon.itp file. Each section (bonds, angle, diherdal, and etc.) has its type. I am wondering if this type (of course, in OPLS-aa case) has the same meaning in the Gromos potentials. As we know, those types for each kind of bonded interactions are well described in the Gromacs manual with clear equations. So, my question is (as I mentioned just above) if this is the same as the OPLS-aa case. Yes, the bond, angle, dihedral types are independent to the underlying force field and correspond to the description in the manual. To make my question clear, I want to give an example. [ bonds ] ... CT HC 1 0.10900 284512.0; CHARMM 22 paramter ... I know the number 1 here means type, which describes what kind of the bonds (strech) between two bonds is used. If this is Gromos potential, I am sure this 1 means harmonic potential according to the Chap. 4 of the Gromacs manual. Is this also applied to OPLS-aa FF? Thank you for your care, again. Sincerely yours, Kim On Fri, 13 Mar 2009, Justin A. Lemkul wrote: Tree wrote: Dear All: I appreciate your answer always. Right now, I am trying to add/modify some values in OPLS-aa FF. I am confused atom type (opls_xxx) and atom name (e.g., C) in atp, bon.itp, and nb.itp files. Please let me try the situation by an example, first. In atp file, ... opls_058 12.01100 ; C in COOR ester JPC3315(91) opls_059 15.99940 ; O= in COOR ester ... In bon.itp file, ... C CA 10.14900 334720.0 ; wlj 8/97 C_2 CA 10.14900 334720.0 ; wlj 8/97 ... In nb.itp file, ... opls_009 C2 7 14.02700 0.000 A 3.90500e-01 4.93712e-01 ; SIG opls_010 C3 6 15.03500 0.000 A 3.90500e-01 7.32200e-01 ; SIG ... I hope you can sense what my question is here. When I define a residue in rtp file, I give some
Re: [gmx-users] Matching atom name and types in OPLS-aa FF
Dear Dr. Periole: Thank you for your answer. That was the point which I wanted to double check (of course after reading the manual...). Thank you again! Sincerely, Kim On Tue, Mar 17, 2009 at 6:09 PM, XAvier Periole x.peri...@rug.nl wrote: On Mar 17, 2009, at 8:45 AM, tree wrote: Dear Justin: Thank you for your email! Thanks to your help and explanation, I am feeling more comfortable with OPLS topology modification. Before this work, I have used Gromacs without modifying FF paramters for simulating 'water' in general systems, which can easily obtained from PDB sites. So, it was not too easy to generate a sort of new topology even I've learned MD. I understand what you meant here. :) I did not mean the selection 1 (Harmonic potential function) is a sort of OPLS-aa FF functions. My question is actually if I can use the Forth power potential when I choose 2 in bond streching section. Since this funtion has different from from 1 (Harmonic potential function), I thought that it may need other paramters that may (may not) be different from the given parameters in OPLS-aa FF. So, my question here is [can I use the Forth power potential for bond strech using the given OPLS-aa paramters?] To that the answer is no! If you change the potential to describe a bond, angle ... the parameters will be different! Have a look a the manual chapter 4. I assume this would be same to others, angle, dihedral, and etc. Thank you again. Sincerely, Kim On Mon, 16 Mar 2009, Justin A. Lemkul wrote: Tree wrote: Dear Dr. Periole: Thank you for your answer. You meant that the types of potential functions do not have any relations with OPLS-aa (except first (1) case). Those (from 2...) are defined as written the Gromacs manual. Table 5.4 defines the different types of intramolecular interactions. You should specify the proper terms based on what corresponds to the force field functional form. That is harmonic potential does not necessarily imply OPLS, but OPLS might imply that you have to use a harmonic potential (because, in fact, many force fields use a harmonic potential for bonds, not just OPLS!) You should refer to the primary literature for the force field, how it was derived, and any subsequent references regarding modifications to the force field. Another option (in addition to doing the background reading!) is to run through some tutorial material with a simple protein under OPLS to get a feel for how an OPLS topology is automatically created by pdb2gmx. -Justin Thank you again. Sincerely, Kim On Mon, Mar 16, 2009 at 5:42 PM, XAvier Periole x.peri...@rug.nlmailto: x.peri...@rug.nl wrote: On Mar 16, 2009, at 9:34 AM, tree wrote: Dear Justin and All: I truly appreciate your clear answer. Since my questions are solved by your explanations, I do not know how I can express my grateful heart. Now I have to ask second step questions. :) It is related to the OPLS-aa bon.itp file. Each section (bonds, angle, diherdal, and etc.) has its type. I am wondering if this type (of course, in OPLS-aa case) has the same meaning in the Gromos potentials. As we know, those types for each kind of bonded interactions are well described in the Gromacs manual with clear equations. So, my question is (as I mentioned just above) if this is the same as the OPLS-aa case. Yes, the bond, angle, dihedral types are independent to the underlying force field and correspond to the description in the manual. To make my question clear, I want to give an example. [ bonds ] ... CT HC 1 0.10900 284512.0; CHARMM 22 paramter ... I know the number 1 here means type, which describes what kind of the bonds (strech) between two bonds is used. If this is Gromos potential, I am sure this 1 means harmonic potential according to the Chap. 4 of the Gromacs manual. Is this also applied to OPLS-aa FF? Thank you for your care, again. Sincerely yours, Kim On Fri, 13 Mar 2009, Justin A. Lemkul wrote: Tree wrote: Dear All: I appreciate your answer always. Right now, I am trying to add/modify some values in OPLS-aa FF. I am confused atom type (opls_xxx) and atom name (e.g., C) in atp, bon.itp, and nb.itp files. Please let me try the situation by an example, first. In atp file, ... opls_058 12.01100 ; C in COOR ester JPC3315(91) opls_059 15.99940 ; O= in COOR ester ... In bon.itp file, ... C CA 10.14900 334720.0 ; wlj 8/97 C_2 CA 10.14900 334720.0 ; wlj 8/97
Re: [gmx-users] Matching atom name and types in OPLS-aa FF
Dear Justin and All: I truly appreciate your clear answer. Since my questions are solved by your explanations, I do not know how I can express my grateful heart. Now I have to ask second step questions. :) It is related to the OPLS-aa bon.itp file. Each section (bonds, angle, diherdal, and etc.) has its type. I am wondering if this type (of course, in OPLS-aa case) has the same meaning in the Gromos potentials. As we know, those types for each kind of bonded interactions are well described in the Gromacs manual with clear equations. So, my question is (as I mentioned just above) if this is the same as the OPLS-aa case. To make my question clear, I want to give an example. [ bonds ] ... CT HC 1 0.10900 284512.0; CHARMM 22 paramter ... I know the number 1 here means type, which describes what kind of the bonds (strech) between two bonds is used. If this is Gromos potential, I am sure this 1 means harmonic potential according to the Chap. 4 of the Gromacs manual. Is this also applied to OPLS-aa FF? Thank you for your care, again. Sincerely yours, Kim On Fri, 13 Mar 2009, Justin A. Lemkul wrote: Tree wrote: Dear All: I appreciate your answer always. Right now, I am trying to add/modify some values in OPLS-aa FF. I am confused atom type (opls_xxx) and atom name (e.g., C) in atp, bon.itp, and nb.itp files. Please let me try the situation by an example, first. In atp file, ... opls_058 12.01100 ; C in COOR ester JPC3315(91) opls_059 15.99940 ; O= in COOR ester ... In bon.itp file, ... C CA 10.14900 334720.0 ; wlj 8/97 C_2 CA 10.14900 334720.0 ; wlj 8/97 ... In nb.itp file, ... opls_009 C2 7 14.02700 0.000 A3.90500e-01 4.93712e-01 ; SIG opls_010 C3 6 15.03500 0.000 A3.90500e-01 7.32200e-01 ; SIG ... I hope you can sense what my question is here. When I define a residue in rtp file, I give some name for my atom in my system and assignment between that specific atom name and opls_xxx. Then, gromacs (pdb2gmx) is using rtp file to assign each atom to the opls_xxx. nb.itp also has opls_xxx information inside, so I can understand how those values are assigned. However, I am not clear how the procedue assign bonded potentials to the system, because bon.itp file does not have any information related to the opls_xxx. It does, but only indirectly. Example, from ffoplsaa.rtp: [ ACE ] [ atoms ] CH3opls_135 -0.180 1 HH31opls_1400.060 1 From ffoplsaanb.itp: opls_135 CT 6 12.01100-0.180 A3.5e-01 2.76144e-01 ... opls_140 HC 1 1.00800 0.060 A2.5e-01 1.25520e-01 So the more literal interpretation of opls_135 is atom type CT, and opls_140 is HC. I assume this is done for convenience. Therefore, in ffoplsaabon.itp: CTHC 10.10900 284512.0 ; CHARMM 22 parameter file Also, my question related to the above sentece is whether the bonded potentials are assigned according to the name of atom, which I defined in my pdb file. (I doubt this... If this question is true, it can't be used for general cases.) Nothing is typically done based on atom names; atom types are much more important when considering bonded and non-bonded potentials. This is subsequently how I can add new values in the bon.itp file by assigning the name in an appropriate way... I think I am relatively clear in assigning between opls_xxx and name in nb.itp file. To summarize my question, how the assignment between opls_xxx and name in the bon.itp can be defined-? Translate the opls_XXX atom types to a more literal type given in ffoplsaanb.itp. -Justin I hope my question and Englsh are clear enough... Thank you again! Sincerely, Kim ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http
Re: [gmx-users] Matching atom name and types in OPLS-aa FF
Dear Dr. Periole: Thank you for your answer. You meant that the types of potential functions do not have any relations with OPLS-aa (except first (1) case). Those (from 2...) are defined as written the Gromacs manual. Thank you again. Sincerely, Kim On Mon, Mar 16, 2009 at 5:42 PM, XAvier Periole x.peri...@rug.nl wrote: On Mar 16, 2009, at 9:34 AM, tree wrote: Dear Justin and All: I truly appreciate your clear answer. Since my questions are solved by your explanations, I do not know how I can express my grateful heart. Now I have to ask second step questions. :) It is related to the OPLS-aa bon.itp file. Each section (bonds, angle, diherdal, and etc.) has its type. I am wondering if this type (of course, in OPLS-aa case) has the same meaning in the Gromos potentials. As we know, those types for each kind of bonded interactions are well described in the Gromacs manual with clear equations. So, my question is (as I mentioned just above) if this is the same as the OPLS-aa case. Yes, the bond, angle, dihedral types are independent to the underlying force field and correspond to the description in the manual. To make my question clear, I want to give an example. [ bonds ] ... CT HC 1 0.10900 284512.0; CHARMM 22 paramter ... I know the number 1 here means type, which describes what kind of the bonds (strech) between two bonds is used. If this is Gromos potential, I am sure this 1 means harmonic potential according to the Chap. 4 of the Gromacs manual. Is this also applied to OPLS-aa FF? Thank you for your care, again. Sincerely yours, Kim On Fri, 13 Mar 2009, Justin A. Lemkul wrote: Tree wrote: Dear All: I appreciate your answer always. Right now, I am trying to add/modify some values in OPLS-aa FF. I am confused atom type (opls_xxx) and atom name (e.g., C) in atp, bon.itp, and nb.itp files. Please let me try the situation by an example, first. In atp file, ... opls_058 12.01100 ; C in COOR ester JPC3315(91) opls_059 15.99940 ; O= in COOR ester ... In bon.itp file, ... C CA 10.14900 334720.0 ; wlj 8/97 C_2 CA 10.14900 334720.0 ; wlj 8/97 ... In nb.itp file, ... opls_009 C2 7 14.02700 0.000 A3.90500e-01 4.93712e-01 ; SIG opls_010 C3 6 15.03500 0.000 A3.90500e-01 7.32200e-01 ; SIG ... I hope you can sense what my question is here. When I define a residue in rtp file, I give some name for my atom in my system and assignment between that specific atom name and opls_xxx. Then, gromacs (pdb2gmx) is using rtp file to assign each atom to the opls_xxx. nb.itp also has opls_xxx information inside, so I can understand how those values are assigned. However, I am not clear how the procedue assign bonded potentials to the system, because bon.itp file does not have any information related to the opls_xxx. It does, but only indirectly. Example, from ffoplsaa.rtp: [ ACE ] [ atoms ] CH3opls_135 -0.180 1 HH31opls_1400.060 1 From ffoplsaanb.itp: opls_135 CT 6 12.01100-0.180 A3.5e-01 2.76144e-01 ... opls_140 HC 1 1.00800 0.060 A2.5e-01 1.25520e-01 So the more literal interpretation of opls_135 is atom type CT, and opls_140 is HC. I assume this is done for convenience. Therefore, in ffoplsaabon.itp: CTHC 10.10900 284512.0 ; CHARMM 22 parameter file Also, my question related to the above sentece is whether the bonded potentials are assigned according to the name of atom, which I defined in my pdb file. (I doubt this... If this question is true, it can't be used for general cases.) Nothing is typically done based on atom names; atom types are much more important when considering bonded and non-bonded potentials. This is subsequently how I can add new values in the bon.itp file by assigning the name in an appropriate way... I think I am relatively clear in assigning between opls_xxx and name in nb.itp file. To summarize my question, how the assignment between opls_xxx and name in the bon.itp can be defined-? Translate the opls_XXX atom types to a more literal type given in ffoplsaanb.itp. -Justin I hope my question and Englsh are clear enough... Thank you again! Sincerely, Kim ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar
[gmx-users] Matching atom name and types in OPLS-aa FF
Dear All: I appreciate your answer always. Right now, I am trying to add/modify some values in OPLS-aa FF. I am confused atom type (opls_xxx) and atom name (e.g., C) in atp, bon.itp, and nb.itp files. Please let me try the situation by an example, first. In atp file, ... opls_058 12.01100 ; C in COOR ester JPC3315(91) opls_059 15.99940 ; O= in COOR ester ... In bon.itp file, ... C CA 10.14900 334720.0 ; wlj 8/97 C_2 CA 10.14900 334720.0 ; wlj 8/97 ... In nb.itp file, ... opls_009 C2 7 14.02700 0.000 A3.90500e-01 4.93712e-01 ; SIG opls_010 C3 6 15.03500 0.000 A3.90500e-01 7.32200e-01 ; SIG ... I hope you can sense what my question is here. When I define a residue in rtp file, I give some name for my atom in my system and assignment between that specific atom name and opls_xxx. Then, gromacs (pdb2gmx) is using rtp file to assign each atom to the opls_xxx. nb.itp also has opls_xxx information inside, so I can understand how those values are assigned. However, I am not clear how the procedue assign bonded potentials to the system, because bon.itp file does not have any information related to the opls_xxx. Also, my question related to the above sentece is whether the bonded potentials are assigned according to the name of atom, which I defined in my pdb file. (I doubt this... If this question is true, it can't be used for general cases.) This is subsequently how I can add new values in the bon.itp file by assigning the name in an appropriate way... I think I am relatively clear in assigning between opls_xxx and name in nb.itp file. To summarize my question, how the assignment between opls_xxx and name in the bon.itp can be defined-? I hope my question and Englsh are clear enough... Thank you again! Sincerely, Kim ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Fwd: Matching atom name and types in OPLS-aa FF
Since I cannot see my message on the gmx-users mail list, I am forwarding this again.I am sorry to bother your email box again... Hope you would understand... -- Forwarded message -- From: Tree tree@gmail.com Date: Fri, Mar 13, 2009 at 8:51 PM Subject: Matching atom name and types in OPLS-aa FF To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Chansoo Kim tree@gmail.com Dear All: I appreciate your answer always. Right now, I am trying to add/modify some values in OPLS-aa FF. I am confused atom type (opls_xxx) and atom name (e.g., C) in atp, bon.itp, and nb.itp files. Please let me try the situation by an example, first. In atp file, ... opls_058 12.01100 ; C in COOR ester JPC3315(91) opls_059 15.99940 ; O= in COOR ester ... In bon.itp file, ... C CA 10.14900 334720.0 ; wlj 8/97 C_2 CA 10.14900 334720.0 ; wlj 8/97 ... In nb.itp file, ... opls_009 C2 7 14.02700 0.000 A3.90500e-01 4.93712e-01 ; SIG opls_010 C3 6 15.03500 0.000 A3.90500e-01 7.32200e-01 ; SIG ... I hope you can sense what my question is here. When I define a residue in rtp file, I give some name for my atom in my system and assignment between that specific atom name and opls_xxx. Then, gromacs (pdb2gmx) is using rtp file to assign each atom to the opls_xxx. nb.itp also has opls_xxx information inside, so I can understand how those values are assigned. However, I am not clear how the procedue assign bonded potentials to the system, because bon.itp file does not have any information related to the opls_xxx. Also, my question related to the above sentece is whether the bonded potentials are assigned according to the name of atom, which I defined in my pdb file. (I doubt this... If this question is true, it can't be used for general cases.) This is subsequently how I can add new values in the bon.itp file by assigning the name in an appropriate way... I think I am relatively clear in assigning between opls_xxx and name in nb.itp file. To summarize my question, how the assignment between opls_xxx and name in the bon.itp can be defined-? I hope my question and Englsh are clear enough... Thank you again! Sincerely, Kim ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Force Field - Gromos96
Dear All: I appreciate it if it would be possible for me to have an answer related to Gromos96 force field. I am hoping to know if the Gromos96 force field can support All-Atom calculation? (Or does it 'only' support Unified Atom simulation?) Thank you for your care! Sincerely, C Kim ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Fwd: Force Field - Gromos96
-- Forwarded message -- From: tree tree@gmail.com Date: Thu, Mar 12, 2009 at 10:09 PM Subject: Force Field - Gromos96 To: gmx-users@gromacs.org Dear All: I appreciate it if it would be possible for me to have an answer related to Gromos96 force field. I am hoping to know if the Gromos96 force field can support All-Atom calculation? (Or does it 'only' support Unified Atom simulation?) Thank you for your care! Sincerely, C Kim ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Polymer entanglement simulation
Dear Users: Hello? As you might know, I am trying to simulate polymer chains with gromacs. Thanks to Justin's large help, I can build topology, which is the essential to actually run the MD. After getting the MD result, I have a serious question. For polymer, as same as the other biopolymers, I assigned potential parameters for 1) bond (stretch), 2) angle, 3) dihedral, 3) improper values. I believe the grompp was working well, because there was no error message at all. After doing a set of actual simulations with my tpr file (and I've checked the processed topology file), unfortunately I could not see any entanglement motion. That motion, I believe, should consist of bond, angle, dihedral, improper, as we see in protein simulations. In this case, would you please explain what I have done wrong...? I guessed that the processed force filed (generated by grompp) could be a problem, but according to Justin's explanations I think it is okay. Please help me! (Hopefully I am becoming more prepared for a real polymer simulation guy...) Thank you! Sincerely, C Kim ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Polymer entanglement simulation
Dear Justin and Users: Thank you for your fast reply. First, I want to clarify the entanglement, so I can get more accurate consult from you! :) Of course, the non-bonded interaction makes entanglement among polymer chains. However, Entanglement here means the intrachain (intramolecular) one. In other words, one chain polymer (having enough monomers inside, e.g. 1 chain polymer containing 20 monomers) can be entangled with itself. This is the reason that I gave force filed parameters related to the bond (stretch), angle, dihedral, and improper dihedral. This is also reason that I have suspected the topology file, which assign force field... In addition, I am putting my setting here. Beginning title= Poly cpp = /lib/cpp include = -I../top define = integrator = md dt = 0.002 nsteps = 50 nstxout = 5000 nstvout = 5000 nstlog = 5000 nstenergy= 250 nstxtcout= 250 xtc_groups = System energygrps = System nstlist = 10 ns_type = grid rlist= 0.7 coulombtype = cut-off rcoulomb = 0.9 rvdw = 0.8 tcoupl = Berendsen tc-grps = carbon hydrogen energygrps = carbon hydrogen tau_t= 0.1 0.1 ref_t= 300 300 Pcoupl = Berendsen tau_p= 1.0 compressibility = 4.5e-5 ref_p= 1.0 gen_vel = no gen_temp = 300 gen_seed = 173529 constraints = all-bonds Ends Thank you, always! Sincerely, C. Kim On Sat, Mar 7, 2009 at 2:19 PM, Justin A. Lemkul jalem...@vt.edu wrote: Tree wrote: Dear Users: Hello? As you might know, I am trying to simulate polymer chains with gromacs. Thanks to Justin's large help, I can build topology, which is the essential to actually run the MD. After getting the MD result, I have a serious question. For polymer, as same as the other biopolymers, I assigned potential parameters for 1) bond (stretch), 2) angle, 3) dihedral, 3) improper values. I believe the grompp was working well, because there was no error message at all. After doing a set of actual simulations with my tpr file (and I've checked the processed topology file), unfortunately I could not see any entanglement motion. That motion, I believe, should consist of bond, angle, dihedral, improper, as we see in protein simulations. Entanglement between chains? That would be a result on nonbonded interactions between (or among) the chains. In this case, would you please explain what I have done wrong...? I guessed that the processed force filed (generated by grompp) could be a problem, but according to Justin's explanations I think it is okay. The processed topology is not generating a problem, per se. Whether or not the force field parameters you are using (i.e., those from OPLS-AA) are appropriate or not is what is the real question. How long are you simulating? It may be a question of timeframe. To equilibrate large polymers may take tens (if not hundreds) of nanoseconds. Another source of error could be the parameters you are specifying in your .mdp file. If you post that, we might be able to tell if there are any errors or inappropriate settings. More than likely, this is a simple question of timeframe and appropriate sampling, which is the inherent limitation in any MD simulation. -Justin Please help me! (Hopefully I am becoming more prepared for a real polymer simulation guy...) Thank you! Sincerely, C Kim ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http
Re: [gmx-users] Polymer entanglement simulation
Dear Justin and Mark: Thank you for your reply. Okay, regarding the 'entanglement' of a polymer, I can ask in a different way, maybe. In a protein simulation, I've seen the motion of 'one' protein macromolecule such as a sort of vibrating, folding, moving around, or changing its shape (becoming thinner, thicker, spherical, or column, etc...). I understand that is originated from potentials defined as 'bond (stretch)', 'angle', 'dihedrals' and 'improper dihedrals', which are different from metal simulation. So, my questions is whether this understanding is correct or not... If not, I hope to learn how those potentials work for the one macromolecule. Since I can a result anyway, I thought it was okay... :) Right, I've changed the cutoff range with a artificial (and arbitrary) guess... As suggested by Justin, I will change mdp file and increase the time duration. If I get a good(?) result, I will post-! Thank you so much. Sincerely yours, Chansoo On Sat, Mar 7, 2009 at 5:45 PM, Justin A. Lemkul jalem...@vt.edu wrote: Mark Abraham wrote: - Original Message - From: Tree tree@gmail.com Date: Sunday, March 8, 2009 6:35 Subject: Re: [gmx-users] Polymer entanglement simulation To: jalem...@vt.edu, Discussion list for GROMACS users gmx-users@gromacs.org Dear Justin and Users: Thank you for your fast reply. First, I want to clarify the entanglement, so I can get more accurate consult from you! :) Of course, the non-bonded interaction makes entanglement among polymer chains. However, Entanglement here means the intrachain (intramolecular) one. In other words, one chain polymer (having enough monomers inside, e.g. 1 chain polymer containing 20 monomers) can be entangled with itself. This is the reason that I gave force filed parameters related to the bond (stretch), angle, dihedral, and improper dihedral. I don't understand what you mean by entanglement, nor what this has to do with your force field parameters. This is also reason that I have suspected the topology file, which assign force field... In addition, I am putting my setting here. tc-grps = carbon hydrogen This is a train wreck waiting to happen. Please consider doing some more background reading and/or tutorial material :-) As is using cut-off for electrostatics, with the bizarre cutoff's you've defined (rlist, rcoulomb, rvdw). Use PME with at least a 1.0-nm cutoff for all three and see if you get better results. Furthermore, as I said before, timeframe might be an issue. 1 ns is not nearly long enough to see such behavior. Try tens of nanoseconds, if not more. -Justin 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] How to define stretch in ffoplsaabon.itp ?
Dear All: *[1 - Situation]* I am trying to define stretch between two bonded atoms (for example, in my system PE (polyethylene), C-C). *[2 - ffoplsaa.rtp file]* In ffoplsaa.rtp file, I assigned C1 opls_136 C2 opls_135 This can be done by my own idea, so it does not bother anything. And totally okay. *[3 - opls_xxx and atom type]* I found that the oplsaa interpret those opls_xxx atoms to atom types (which are in ffoplsaabon.itp file) as follows, opls_136 CT opls_135 CT. ( from a file containing opls_136 CT 6 12.01100-0.120 A3.5e-01 2.76144e-01 opls_137 CT 6 12.01100-0.060 A3.5e-01 2.76144e-01 ) *[4 - ffoplsaabon.itp]* Based on the information in the section [2] and [3] above, I added following two sentences in the ffoplsaabon.itp file. [ bondtypes ] ; ij func b0 kb CTCT 10.14900 334720.0 ; *[5 - pdb2gmx result]* Until the section [4], I have new ffoplsaabon.itp file, so I ran pdb2gmx for my PE system. After that, when I looked at the topology file (e.g. topol.top), I could not find any information in the [ bonds ] section (after the [ atoms ] section). In other words, topol.top shows nothing in [ bonds ] section. [ bonds ] ; aiaj functc0c1c2 c3 1 2 1 *[6 - Question!]* I think my mistake came from section [3] or [4]. (1) Would you please let me know what I did wrong...? (2) If someone is familiar with defining stretch, angle, dihedral and torsion in ffoplsaabon.itp, would you please give me an idea on how-to? (3) Would you please summarize how the gromacs maps opls_xxx with atom type (C, CT... etc)? *[7 - Thank you!]* Thank you so much your participation and help!!! Sincerely, Kim ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Fwd: How to define stretch in ffoplsaabon.itp ?
In the section [3], the file is csoplsaanb.itp. In the file, I found how an opls_xxx is assigned to an atom type. (If this is a CORRECT approach...) Thank you! Sincerely, C. Kim -- Forwarded message -- From: Tree tree@gmail.com Date: Wed, Mar 4, 2009 at 9:38 AM Subject: How to define stretch in ffoplsaabon.itp ? To: Discussion list for GROMACS users gmx-users@gromacs.org Dear All: *[1 - Situation]* I am trying to define stretch between two bonded atoms (for example, in my system PE (polyethylene), C-C). *[2 - ffoplsaa.rtp file]* In ffoplsaa.rtp file, I assigned C1 opls_136 C2 opls_135 This can be done by my own idea, so it does not bother anything. And totally okay. *[3 - opls_xxx and atom type]* I found that the oplsaa interpret those opls_xxx atoms to atom types (which are in ffoplsaabon.itp file) as follows, opls_136 CT opls_135 CT. ( from a file containing opls_136 CT 6 12.01100-0.120 A3.5e-01 2.76144e-01 opls_137 CT 6 12.01100-0.060 A3.5e-01 2.76144e-01 ) *[4 - ffoplsaabon.itp]* Based on the information in the section [2] and [3] above, I added following two sentences in the ffoplsaabon.itp file. [ bondtypes ] ; ij func b0 kb CTCT 10.14900 334720.0 ; *[5 - pdb2gmx result]* Until the section [4], I have new ffoplsaabon.itp file, so I ran pdb2gmx for my PE system. After that, when I looked at the topology file (e.g. topol.top), I could not find any information in the [ bonds ] section (after the [ atoms ] section). In other words, topol.top shows nothing in [ bonds ] section. [ bonds ] ; aiaj functc0c1c2 c3 1 2 1 *[6 - Question!]* I think my mistake came from section [3] or [4]. (1) Would you please let me know what I did wrong...? (2) If someone is familiar with defining stretch, angle, dihedral and torsion in ffoplsaabon.itp, would you please give me an idea on how-to? (3) Would you please summarize how the gromacs maps opls_xxx with atom type (C, CT... etc)? *[7 - Thank you!]* Thank you so much your participation and help!!! Sincerely, Kim ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How to define stretch in ffoplsaabon.itp ?
Dear Justin: Thank you for your answer!! Yes, I found there is already a bond defined for CT and CT, meanwhile I am waiting response from gmx-uses. I deleted mine! To confirm, I cannot avoid to ask you a question again. So, please let me explain... Sections [ bonds ], [pairs], [angles] and etc. in the topol.top show the information on what interaction (and how) exist among atoms in those sections. Real potential values are interpreted (assigned) when I run grompp to get tpr file. --- Is this right? If this is right, I do not understand why I am not able to have new topol_new.top file when I use -pp topol_new.top with grompp. There is no error message... --- What does the -pp option generate when doing grompp-? Regarding the assignment of opls_xxx to atom type is, I think, well described in the file, csoplsaanb.itp. Thank you again! Sincerely C Kim On Wed, Mar 4, 2009 at 9:47 AM, Justin A. Lemkul jalem...@vt.edu wrote: Tree wrote: Dear All: *[1 - Situation]* I am trying to define stretch between two bonded atoms (for example, in my system PE (polyethylene), C-C). *[2 - ffoplsaa.rtp file]* In ffoplsaa.rtp file, I assigned C1 opls_136 C2 opls_135 This can be done by my own idea, so it does not bother anything. And totally okay. *[3 - opls_xxx and atom type]* I found that the oplsaa interpret those opls_xxx atoms to atom types (which are in ffoplsaabon.itp file) as follows, opls_136 CT opls_135 CT. ( from a file containing opls_136 CT 6 12.01100-0.120 A 3.5e-01 2.76144e-01 opls_137 CT 6 12.01100-0.060 A3.5e-01 2.76144e-01 ) *[4 - ffoplsaabon.itp]* Based on the information in the section [2] and [3] above, I added following two sentences in the ffoplsaabon.itp file. [ bondtypes ] ; ij func b0 kb CTCT 10.14900 334720.0 ; There is already a CT-CT bond defined in ffoplsaabon.itp: CTCT 10.15290 224262.4 ; CHARMM 22 parameter file If you don't want those parameters, make sure you comment out that line so you know which parameters you are actually using! *[5 - pdb2gmx result]* Until the section [4], I have new ffoplsaabon.itp file, so I ran pdb2gmx for my PE system. After that, when I looked at the topology file (e.g. topol.top), I could not find any information in the [ bonds ] section (after the [ atoms ] section). In other words, topol.top shows nothing in [ bonds ] section. [ bonds ] ; aiaj functc0c1c2 c3 1 2 1 It's not showing nothing. Atoms 1 and 2 are bonded together. As long as there are parameters defined in ffoplsaabon.itp, then grompp will interpret the topology correctly. If grompp fails, then you have identified a problem. *[6 - Question!]* I think my mistake came from section [3] or [4]. (1) Would you please let me know what I did wrong...? Nothing so far that I can see (aside from potentially duplicating parameters). (2) If someone is familiar with defining stretch, angle, dihedral and torsion in ffoplsaabon.itp, would you please give me an idea on how-to? How do you define stretch? The force constant for how much the bond length can deviate? Otherwise, all bonded parameters are assigned by pdb2gmx as long as all atom types are defined. (3) Would you please summarize how the gromacs maps opls_xxx with atom type (C, CT... etc)? Read ffoplsaa.atp. -Justin *[7 - Thank you!]* Thank you so much your participation and help!!! Sincerely, Kim ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman
Re: [gmx-users] How to define stretch in ffoplsaabon.itp ?
Dear Justin: On Wed, Mar 4, 2009 at 10:04 AM, Justin A. Lemkul jalem...@vt.edu wrote: Tree wrote: Dear Justin: Thank you for your answer!! Yes, I found there is already a bond defined for CT and CT, meanwhile I am waiting response from gmx-uses. I deleted mine! To confirm, I cannot avoid to ask you a question again. So, please let me explain... Sections [ bonds ], [pairs], [angles] and etc. in the topol.top show the information on what interaction (and how) exist among atoms in those sections. Real potential values are interpreted (assigned) when I run grompp to get tpr file. --- Is this right? Yes. If this is right, I do not understand why I am not able to have new topol_new.top file when I use -pp topol_new.top with grompp. There is no error message... It isn't produced? It is produced. However, it seems having ALL the informations from '.atp', 'bon.itp' and 'nb.itp'... Since I guessed that I would get a processed topology file having information, which was blank in the original topology file, this looks pretty weird... --- What does the -pp option generate when doing grompp-? The -pp option gives you a processed topology, explicitly showing every parameter that grompp assembled. Yes... That is what I understood... Since I do not think I had an appropriate processed topology, I guessed that there may be different meaning. Thank you for your confirmation. Regarding the assignment of opls_xxx to atom type is, I think, well described in the file, csoplsaanb.itp. Is that some sort of modified form of ffoplsaanb.itp? Often times a more detailed explanation is found in the .atp file for the corresponding force field. -Justin Thank you again! Sincerely C Kim On Wed, Mar 4, 2009 at 9:47 AM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Tree wrote: Dear All: *[1 - Situation]* I am trying to define stretch between two bonded atoms (for example, in my system PE (polyethylene), C-C). *[2 - ffoplsaa.rtp file]* In ffoplsaa.rtp file, I assigned C1 opls_136 C2 opls_135 This can be done by my own idea, so it does not bother anything. And totally okay. *[3 - opls_xxx and atom type]* I found that the oplsaa interpret those opls_xxx atoms to atom types (which are in ffoplsaabon.itp file) as follows, opls_136 CT opls_135 CT. ( from a file containing opls_136 CT 6 12.01100 -0.120 A3.5e-01 2.76144e-01 opls_137 CT 6 12.01100-0.060 A3.5e-01 2.76144e-01 ) *[4 - ffoplsaabon.itp]* Based on the information in the section [2] and [3] above, I added following two sentences in the ffoplsaabon.itp file. [ bondtypes ] ; ij func b0 kb CTCT 10.14900 334720.0 ; There is already a CT-CT bond defined in ffoplsaabon.itp: CTCT 10.15290 224262.4 ; CHARMM 22 parameter file If you don't want those parameters, make sure you comment out that line so you know which parameters you are actually using! *[5 - pdb2gmx result]* Until the section [4], I have new ffoplsaabon.itp file, so I ran pdb2gmx for my PE system. After that, when I looked at the topology file (e.g. topol.top), I could not find any information in the [ bonds ] section (after the [ atoms ] section). In other words, topol.top shows nothing in [ bonds ] section. [ bonds ] ; aiaj functc0c1c2 c3 1 2 1 It's not showing nothing. Atoms 1 and 2 are bonded together. As long as there are parameters defined in ffoplsaabon.itp, then grompp will interpret the topology correctly. If grompp fails, then you have identified a problem. *[6 - Question!]* I think my mistake came from section [3] or [4]. (1) Would you please let me know what I did wrong...? Nothing so far that I can see (aside from potentially duplicating parameters). (2) If someone is familiar with defining stretch, angle, dihedral and torsion in ffoplsaabon.itp, would you please give me an idea on how-to? How do you define stretch? The force constant for how much the bond length can deviate? Otherwise, all bonded parameters are assigned by pdb2gmx as long as all atom types are defined. (3) Would you please summarize how the gromacs maps opls_xxx with atom type (C, CT... etc)? Read ffoplsaa.atp. -Justin *[7 - Thank you!]* Thank you so much your participation and help!!! Sincerely, Kim
Fwd: [gmx-users] How to define stretch in ffoplsaabon.itp ?
Dear Justin and All : As I mentioned below, I want to check if my processed topology (by grompp) is right or not. Therefore, 1) What does the processed topology file normally have inside-? 2) Is it right if the processed topology has *ALL* of the information from oplsaa.rtp and opls*.itp. Thank you! Sincerely yours, C Kim -- Forwarded message -- From: Tree tree@gmail.com Date: Wed, Mar 4, 2009 at 10:11 AM Subject: Re: [gmx-users] How to define stretch in ffoplsaabon.itp ? To: Discussion list for GROMACS users gmx-users@gromacs.org Dear Justin: On Wed, Mar 4, 2009 at 10:04 AM, Justin A. Lemkul jalem...@vt.edu wrote: Tree wrote: Dear Justin: Thank you for your answer!! Yes, I found there is already a bond defined for CT and CT, meanwhile I am waiting response from gmx-uses. I deleted mine! To confirm, I cannot avoid to ask you a question again. So, please let me explain... Sections [ bonds ], [pairs], [angles] and etc. in the topol.top show the information on what interaction (and how) exist among atoms in those sections. Real potential values are interpreted (assigned) when I run grompp to get tpr file. --- Is this right? Yes. If this is right, I do not understand why I am not able to have new topol_new.top file when I use -pp topol_new.top with grompp. There is no error message... It isn't produced? It is produced. However, it seems having ALL the informations from '.atp', 'bon.itp' and 'nb.itp'... Since I guessed that I would get a processed topology file having information, which was blank in the original topology file, this looks pretty weird... --- What does the -pp option generate when doing grompp-? The -pp option gives you a processed topology, explicitly showing every parameter that grompp assembled. Yes... That is what I understood... Since I do not think I had an appropriate processed topology, I guessed that there may be different meaning. Thank you for your confirmation. Regarding the assignment of opls_xxx to atom type is, I think, well described in the file, csoplsaanb.itp. Is that some sort of modified form of ffoplsaanb.itp? Often times a more detailed explanation is found in the .atp file for the corresponding force field. -Justin Thank you again! Sincerely C Kim On Wed, Mar 4, 2009 at 9:47 AM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Tree wrote: Dear All: *[1 - Situation]* I am trying to define stretch between two bonded atoms (for example, in my system PE (polyethylene), C-C). *[2 - ffoplsaa.rtp file]* In ffoplsaa.rtp file, I assigned C1 opls_136 C2 opls_135 This can be done by my own idea, so it does not bother anything. And totally okay. *[3 - opls_xxx and atom type]* I found that the oplsaa interpret those opls_xxx atoms to atom types (which are in ffoplsaabon.itp file) as follows, opls_136 CT opls_135 CT. ( from a file containing opls_136 CT 6 12.01100 -0.120 A3.5e-01 2.76144e-01 opls_137 CT 6 12.01100-0.060 A3.5e-01 2.76144e-01 ) *[4 - ffoplsaabon.itp]* Based on the information in the section [2] and [3] above, I added following two sentences in the ffoplsaabon.itp file. [ bondtypes ] ; ij func b0 kb CTCT 10.14900 334720.0 ; There is already a CT-CT bond defined in ffoplsaabon.itp: CTCT 10.15290 224262.4 ; CHARMM 22 parameter file If you don't want those parameters, make sure you comment out that line so you know which parameters you are actually using! *[5 - pdb2gmx result]* Until the section [4], I have new ffoplsaabon.itp file, so I ran pdb2gmx for my PE system. After that, when I looked at the topology file (e.g. topol.top), I could not find any information in the [ bonds ] section (after the [ atoms ] section). In other words, topol.top shows nothing in [ bonds ] section. [ bonds ] ; aiaj functc0c1c2 c3 1 2 1 It's not showing nothing. Atoms 1 and 2 are bonded together. As long as there are parameters defined in ffoplsaabon.itp, then grompp will interpret the topology correctly. If grompp fails, then you have identified a problem. *[6 - Question!]* I think my mistake came from section [3] or [4]. (1) Would you please let me know what I did wrong...? Nothing so far that I can see (aside from potentially duplicating parameters). (2) If someone is familiar with defining stretch, angle, dihedral and torsion in ffoplsaabon.itp, would you
