Re: [gmx-users] regarding nacl simulation in water using tabulated potentials
i had followed the instructions in themnaual for ninbonded interactions adn had created two tables one for nacl adn other table for water ion interations...i wanted some information on how to use these tables for starting thee simulation On Mon, May 9, 2011 at 11:20 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 9/05/2011 3:46 PM, sreelakshmi ramesh wrote: dear gmx users, i have to simulate nacl in water...the system is acubic box with just one na adn one cl ion in tip3p water.i wanted to use a buckingham potential for na adn cl interaction and lennard jones for water -ion intercation.i really dont have any idea on how to do this.any help will be of great use for me... Can't be done simply. You'd have to use non-bonded interaction tables for the Na-Cl interaction with properly constructed energy groups. Search the manual and webpage for details. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] regarding nacl simulation in water using tabulated potentials
On 9/05/2011 4:01 PM, sreelakshmi ramesh wrote: i had followed the instructions in themnaual for ninbonded interactions adn had created two tables one for nacl adn other table for water ion interations... That's not I really don't have any idea on how to do this. Please ask the question you want answered, or you're wasting everyone's time. i wanted some information on how to use these tables for starting thee simulation Sorry, that's too general. You might want help with a command line, or setting up the .mdp, or something else. Please read 6.7 of the manual, try things, and ask a focused question. Mark On Mon, May 9, 2011 at 11:20 AM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 9/05/2011 3:46 PM, sreelakshmi ramesh wrote: dear gmx users, i have to simulate nacl in water...the system is acubic box with just one na adn one cl ion in tip3p water.i wanted to use a buckingham potential for na adn cl interaction and lennard jones for water -ion intercation.i really dont have any idea on how to do this.any help will be of great use for me... Can't be done simply. You'd have to use non-bonded interaction tables for the Na-Cl interaction with properly constructed energy groups. Search the manual and webpage for details. Mark -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] freeze the carbonyl carbon atoms
Hi: I have a carbon nanotube (CNT) and several carbonly groups (C=O). Meanwhile the carbonly carbon atoms are part of the CNT. That is to say an oxygen atom is attached to one carbon atom of the CNT to form a carbonyl group. All the carbon atoms are supposed to be fixed, while carbonyl carbon and oxygen atoms are supposed to have bond interactions. I can freeze the rest carbon atoms of the CNT, but how to deal with the carbonly atoms? Any suggestions are appreciated! Thank you in advance! 2011-05-09 toby1024 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] sphere around a protein
shivangi nangia wrote: Hi Justin, I used 15 nm cubic box and 6 nm shell. I again tried to insert only 1 histidine molecule in the sphere. I get the same error Fatal error: One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than the cut-off. Please provide the exact command that gives the error. I cannot reproduce this using a shell value less than half a box vector. You may also want to try starting from a clean directory - get rid of old files and intermediates so you're sure you're using the right files. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] problem while running grompp command
rashi parihar wrote: Hi all. I am doing dynamics studies of protein-ligand dynamics.When I am running grompp command error is coming atomtype SDMSO NOT FOUND . I checked in drg.itp file [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 OM 1 LIG OXT 1 -0.758 15.9994 2 C 1 LIG C 1 0.362 12.0110 3 OM 1 LIG O 1 -0.758 15.9994 4 CH1 1 LIG CA 1 0.154 13.0190 5 NL 1 LIG N 2 0.590 14.0067 6 H 1 LIG H3 2 0.001 1.0080 7 H 1 LIG H4 2 0.002 1.0080 8 H 1 LIG H1 2 0.002 1.0080 9 CH2 1 LIG CB 2 0.109 14.0270 10 CH2 1 LIG CG 2 0.109 14.0270 11 SDMSO 1 LIG SD 2 0.974 32.0600 now in 11th row SDMSO IS PRESENT.How can I solve this problem?plz help me!!! The problem is that your topology file is calling SDMSO, which does not exist. All Gromos force fields use SDmso - capitalization matters. Check the .atp file for your chosen force field to be sure of the requirements of the force field. It looks to me like this is a PRODRG output. Please see the paper linked from http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips as to why you should likely not use this topology in its current state for anything. -Justin -- images[12] “Many Smiles Begin Because Of Another Smile . . . . Regards, Rashi -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] freeze the carbonyl carbon atoms
toby1024 wrote: Hi: I have a carbon nanotube (CNT) and several carbonly groups (C=O). Meanwhile the carbonly carbon atoms are part of the CNT. That is to say an oxygen atom is attached to one carbon atom of the CNT to form a carbonyl group. All the carbon atoms are supposed to be fixed, while carbonyl carbon and oxygen atoms are supposed to have bond interactions. I can freeze the rest carbon atoms of the CNT, but how to deal with the carbonly atoms? By fixed, do you mean their positions should be invariant (i.e. freeze groups) or that their bond lengths should be constrained? If the former, then you should be able to make use of index groups to define an appropriate freezegrp in the .mdp file. If the latter, use constraints = none in the .mdp file, and write a [constraints] directive for the bonds you do wish to be constrained. -Justin Any suggestions are appreciated! Thank you in advance! 2011-05-09 toby1024 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: gmx-users Digest, Vol 85, Issue 65
Hi Prof. Mark Abraham I recived a tutorial from you that in the tutorial 3th molecule was one and there is not some of the 3th molecules that distributed randomly. I will be very thankful if you introduce to me a tutorial about my work. Thanks alot Maria On Mon, May 9, 2011 at 11:37 AM, gmx-users-requ...@gromacs.org wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. regarding creating tabulated potentials (sreelakshmi ramesh) 2. Re: Re: gmx-users Digest, Vol 85, Issue 61 (Mark Abraham) 3. regarding nacl simulation in water using tabulatedpotentials (sreelakshmi ramesh) 4. Re: RE: gmx-users Digest, Vol 85, Issue 53 (Mark Abraham) 5. Re: regarding nacl simulation in water using tabulated potentials (Mark Abraham) 6. Re: regarding nacl simulation in water using tabulated potentials (sreelakshmi ramesh) 7. Re: regarding nacl simulation in water using tabulated potentials (Mark Abraham) -- Message: 1 Date: Mon, 9 May 2011 11:12:20 +0530 From: sreelakshmi ramesh sree.laks...@research.iiit.ac.in Subject: [gmx-users] regarding creating tabulated potentials To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: BANLkTimhMBkb0Ptt4wKCj_Dx=nbxwcq...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 dear gmx users, -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20110509/245ab8d2/attachment-0001.html -- Message: 2 Date: Mon, 09 May 2011 15:45:41 +1000 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] Re: gmx-users Digest, Vol 85, Issue 61 To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4dc77f85.8010...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 9/05/2011 3:40 PM, Maria Hamilton wrote: Hi Dallas Please do not respond to whole digests - it confuses the archive. Cut out the relevant part and reply to it. Also, please choose a meaningful subject line. You said that Easiest way is probably set up the appropriate sized box for molecule 2, randomly distributed molecule 3 in appropriate number through it (genbox), then solvate that box with molecule 2, then combine that box with solvated box containing molecule 1. How can I combine the two different box?Do you know any tutorial for this? Yes, the one on biphasic systems that I suggested two days ago that you search for :-) Mark -- Message: 3 Date: Mon, 9 May 2011 11:16:59 +0530 From: sreelakshmi ramesh sree.laks...@research.iiit.ac.in Subject: [gmx-users] regarding nacl simulation in water using tabulated potentials To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: BANLkTi=upi92tu6dnjxm7oc9xfuk4hj...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 dear gmx users, i have to simulate nacl in water...the system is acubic box with just one na adn one cl ion in tip3p water.i wanted to use a buckingham potential for na adn cl interaction and lennard jones for water -ion intercation.i really dont have any idea on how to do this.any help will be of great use for me... thanks and regards, shree -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20110509/c048df19/attachment-0001.html -- Message: 4 Date: Mon, 09 May 2011 15:47:55 +1000 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] RE: gmx-users Digest, Vol 85, Issue 53 To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4dc7800b.2080...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 9/05/2011 9:10 AM, Ryan S Davis (rsdavis1) wrote: I am not sure if I replied to this thread correctly, but anyway. Please use a relevant subject line. I tried the things you guys suggested, but I still cant get it to work. You were right $HOME does have a slash in front but I am not actually using that variable, just used it in the mailing list for convience, sorry. Copy and paste of actual terminal sessions is always preferable. Computers are literal, and troubleshooting things filtered through people's heads usually wastes time. I reinstalled the libraries, just to make
Re: [gmx-users] liquid/liquid
Maria Hamilton wrote: Hi Prof. Mark Abraham I recived a tutorial from you that in the tutorial 3th molecule was one and there is not some of the 3th molecules that distributed randomly. I will be very thankful if you introduce to me a tutorial about my work. Tutorials are not written to tailor to every possible nuance of a user's desires. They exist to provide you with a basic principle that can be applied to other systems. The workflow is the same - create your heterogeneous layer using the information provided here: http://lists.gromacs.org/pipermail/gmx-users/2011-May/061164.html and here: http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents Then use the basic steps in the biphasic system tutorial to combine whatever layers you like in whatever manner you choose. -Justin Thanks alot Maria -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] ambar to opls force field
Nilesh Dhumal wrote: Hello Justin, In the J. Chem. Phys. paper author have run the simulation 6.5 ns. So I run the simulation 6.5 ns for collecting data and I have total 256 water molecules. I also asked how you calculated the dielectric constant. When trying to replicate others' work, it is often most beneficial and less time-consuming to simply contact the corresponding author of the paper. They can talk with you directly about methodological details. -Justin NIlesh On Sun, May 8, 2011 11:58 pm, Justin A. Lemkul wrote: Nilesh Dhumal wrote: Hello Justin, Here I have done some analysis. The original value reported in J.Chem. Phys. 124, 024503 2006, paper are Kbond = 443153.3808 kJ/mol nm**2 Kangle = 317.5656 kJ/mol rad**2. Below are the results for the dielectric constant of water.I made the .itp file pasted below the table. Bond length is nm. bond length Kbond angleKangledielectric constant 0.1012 443153.3808113.24 317.5656 ~1.9 : orginal value 0.1012 221576.6904113.24 317.5656 ~80 : 1/2 (Kbond) 0.1012 443153.3808113.24 158.7828 ~1.58 : 1/2 (kangle) 0.1012 221576.6904113.24 317.5656 ~1.9 : 1/2 (Kbond)(Kangle) How were these dielectric constants calculated? Did you collect sufficient data? It seems to me that there is no definitive dependence on any of these parameters, and you have one outlying point that is coincidentally close to what you want. A consistently wrong dielectric would suggest that either you're not calculating it right or you don't have sufficiently converged data. Based on a quick look through the paper, it seems to me that your original premise of converting between force fields is not related to the task at hand. Water models are relatively force field-agnostic, especially when trivial functional forms, such as harmonic potentials, are applied. There is nothing fancy here. Given the following: [ bondtypes ] ; ij func b0 kb OWHW 10.1012 443153.3808 ; J. Chem. Phys. (2006),124,024503 [ angletypes ] ; ijk func th0 cth HW OW HW 1 113.24 158.7828 ; J. Chem. Phys. (2006),124,024503 You are indeed applying simple harmonic potentials (see the manual to confirm the form), which again indicates to me that you should not be playing with the force constants in the model described in the paper. Use Ka and Kb as listed. Halving these quantities will result in a harmonic potential, e.g. for bonds of (1/4)Kb(b-b0)^2 rather then the proper coefficient of 1/2. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] git server maintenance downtime
Hi, The git server may be temporarily offline today for maintenance. Cheers, Rossen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] freeze the carbonyl carbon atoms
On 9/05/2011 5:23 PM, toby1024 wrote: Hi: I have a carbon nanotube (CNT) and several carbonly groups (C=O). Meanwhile the carbonly carbon atoms are part of the CNT. That is to say an oxygen atom is attached to one carbon atom of the CNT to form a carbonyl group. All the carbon atoms are supposed to be fixed, while carbonyl carbon and oxygen atoms are supposed to have bond interactions. I can freeze the rest carbon atoms of the CNT, but how to deal with the carbonly atoms? Well if you're prepared to model the CNT frozen, why not freeze the oxygen bound to it? Anything else sounds like a recipe for more trouble. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: gmx-users Digest, Vol 85, Issue 67
I mean all the positions of the carbon atoms are invariant during mdrun. In the .gro file, carbonyl carbon and oxygen atoms are defined as group 'Carbonyl' and the rest every single carbon atom is defined as 'CNT'. For the use of 'freeze groups', the group 'CNT' should be freezed. But for group 'Carbonyl', as oxygen atom is allowed to move, it is not appropriate to freeze group 'Carbonyl'. I wonder whether the same atom can be included in two or more groups. If it can be, I can ignore the group name defined in the .gro file and redefine groups by using command 'make_ndx'. Then I am able to make use of index groups to define an appropriate freezegrp in the .mdp file. All the carbon atoms of the CNT (inclduing carbonyl carbon atoms) are supposed to be defined as 'CNT', and carbonyl carbon atoms and oxygen oxygens are 'Carbonyl'. Group 'CNT' is the freeze group. Is it feasible for this idea? Thank you! 2011-05-09 toby1024 Message: 4 Date: Mon, 09 May 2011 06:58:04 -0400 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] freeze the carbonyl carbon atoms To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4dc7c8bc.5090...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed toby1024 wrote: Hi: I have a carbon nanotube (CNT) and several carbonly groups (C=O). Meanwhile the carbonly carbon atoms are part of the CNT. That is to say an oxygen atom is attached to one carbon atom of the CNT to form a carbonyl group. All the carbon atoms are supposed to be fixed, while carbonyl carbon and oxygen atoms are supposed to have bond interactions. I can freeze the rest carbon atoms of the CNT, but how to deal with the carbonly atoms? By fixed, do you mean their positions should be invariant (i.e. freeze groups) or that their bond lengths should be constrained? If the former, then you should be able to make use of index groups to define an appropriate freezegrp in the .mdp file. If the latter, use constraints = none in the .mdp file, and write a [constraints] directive for the bonds you do wish to be constrained. -Justin Any suggestions are appreciated! Thank you in advance! 2011-05-09 toby1024 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: freeze the carbonyl carbon atoms
I intend to apply an electric filed on the whole system and the possitive oxygen will be certainly affected. 2011-05-09 toby1024 Message: 5 Date: Mon, 09 May 2011 22:38:48 +1000 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] freeze the carbonyl carbon atoms To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4dc7e058.10...@anu.edu.au Content-Type: text/plain; charset=iso-8859-1 On 9/05/2011 5:23 PM, toby1024 wrote: Hi: I have a carbon nanotube (CNT) and several carbonly groups (C=O). Meanwhile the carbonly carbon atoms are part of the CNT. That is to say an oxygen atom is attached to one carbon atom of the CNT to form a carbonyl group. All the carbon atoms are supposed to be fixed, while carbonyl carbon and oxygen atoms are supposed to have bond interactions. I can freeze the rest carbon atoms of the CNT, but how to deal with the carbonly atoms? Well if you're prepared to model the CNT frozen, why not freeze the oxygen bound to it? Anything else sounds like a recipe for more trouble. Mark -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20110509/1fa0aa57/attachment-0001.html -- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] frozen CNT with carbonyls
On 9/05/2011 10:43 PM, toby1024 wrote: Please use a useful subject line when replying to a digest. I mean all the positions of the carbon atoms are invariant during mdrun. In the .gro file, carbonyl carbon and oxygen atoms are defined as group 'Carbonyl' and the rest every single carbon atom is defined as 'CNT'. A .gro file doesn't have groups. For the use of 'freeze groups', the group 'CNT' should be freezed. But for group 'Carbonyl', as oxygen atom is allowed to move, it is not appropriate to freeze group 'Carbonyl'. Sure, I think you want a freeze group of all the nanotube carbons, and all the carbonyl oxygens. make_ndx will allow you make such a union. I wonder whether the same atom can be included in two or more groups. If it can be, I can ignore the group name defined in the .gro file and redefine groups by using command 'make_ndx'. Then I am able to make use of index Groups aren't defined in the coordinate file. If you use a GROMACS utility that can accept an index file as input, and do not provide one, then GROMACS generates some standard ones from the coordinate file. In the case of make_ndx, these are then written out when you quit. groups to define an appropriate freezegrp in the .mdp file. All the carbon atoms of the CNT (inclduing carbonyl carbon atoms) are supposed to be defined as 'CNT', and carbonyl carbon atoms and oxygen oxygens are 'Carbonyl'. Group 'CNT' is the freeze group. Is it feasible for this idea? You're in charge... I don't know what external entity is dictating what you are supposed to do :-) Mark Thank you! 2011-05-09 toby1024 Message: 4 Date: Mon, 09 May 2011 06:58:04 -0400 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] freeze the carbonyl carbon atoms To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4dc7c8bc.5090...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed toby1024 wrote: Hi: I have a carbon nanotube (CNT) and several carbonly groups (C=O). Meanwhile the carbonly carbon atoms are part of the CNT. That is to say an oxygen atom is attached to one carbon atom of the CNT to form a carbonyl group. All the carbon atoms are supposed to be fixed, while carbonyl carbon and oxygen atoms are supposed to have bond interactions. I can freeze the rest carbon atoms of the CNT, but how to deal with the carbonly atoms? By fixed, do you mean their positions should be invariant (i.e. freeze groups) or that their bond lengths should be constrained? If the former, then you should be able to make use of index groups to define an appropriate freezegrp in the .mdp file. If the latter, use constraints = none in the .mdp file, and write a [constraints] directive for the bonds you do wish to be constrained. -Justin Any suggestions are appreciated! Thank you in advance! 2011-05-09 toby1024 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] simulation of a non complete structure
Sajad Ahrari wrote: dear users is it rational to do a simulation on a structure witch is not complete? i mean pdb structure doesn't cover whole of the protein but it's active core domain. may be i should be asking this question somewhere else, but i thought some of you may have concerned with such case and in fact i didn't really know where to ask it! It depends on your aims. If you can answer the question of interest while still neglecting, i.e. missing termini, and you can prove that the missing residues do not play any functional role in the dynamics of the active domain, then maybe you can simulate it. But that is a lot of assumptions. It's certainly been done, but it may require lots of justification and prior proof that no ill effects will exist. Note that this only applies to missing termini. Anything missing within the sequence will cause pdb2gmx to fail, and even if you force it without building a suitable model, mdrun will fail due to a physically unrealistic simulation. -Justin thanks in advance! sajad -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] total force acting on group
Hi dear user's I want to calculate total force acting on one certain atom or group. gromacs dose not have tools for force analysis, and FDA only give pair forces between one group of atoms how can i do this? thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] ambar to opls force field
Nilesh Dhumal wrote: I used g_dipoles to calculate dielectric constant. g_dipoles -f water.trr -s water.tpr -eps Group 0 ( System) has 768 elements Group 1 ( Protein) has 768 elements Group 2 ( Protein-H) has 256 elements Group 3 ( C-alpha) has 0 elements Group 4 (Backbone) has 0 elements Group 5 ( MainChain) has 0 elements Group 6 (MainChain+Cb) has 0 elements Group 7 ( MainChain+H) has 0 elements Group 8 ( SideChain) has 768 elements Group 9 ( SideChain-H) has 256 elements Select a group: 0 I selected 0. The manual and the archive are not clear on the proper way to calculate a dielectric constant, but it seems your use of g_dipoles neglects several terms that may affect your outcome. I would suggest backing up and applying your methodology to a well-defined system like rigid SPC to see if you can recover the proper dielectric constant for that system (65, I believe). That will tell you if your method for calculating the dielectric is correct. If it is, and you still can't reproduce the results for the flexible model, my advice is still to contact the authors of the cited paper for advice. -Justin Nilesh On Mon, May 9, 2011 8:28 am, Justin A. Lemkul wrote: Nilesh Dhumal wrote: Hello Justin, In the J. Chem. Phys. paper author have run the simulation 6.5 ns. So I run the simulation 6.5 ns for collecting data and I have total 256 water molecules. I also asked how you calculated the dielectric constant. When trying to replicate others' work, it is often most beneficial and less time-consuming to simply contact the corresponding author of the paper. They can talk with you directly about methodological details. -Justin NIlesh On Sun, May 8, 2011 11:58 pm, Justin A. Lemkul wrote: Nilesh Dhumal wrote: Hello Justin, Here I have done some analysis. The original value reported in J.Chem. Phys. 124, 024503 2006, paper are Kbond = 443153.3808 kJ/mol nm**2 Kangle = 317.5656 kJ/mol rad**2. Below are the results for the dielectric constant of water.I made the .itp file pasted below the table. Bond length is nm. bond length Kbond angleKangledielectric constant 0.1012 443153.3808113.24 317.5656 ~1.9 : orginal value 0.1012 221576.6904113.24 317.5656 ~80 : 1/2 (Kbond) 0.1012 443153.3808113.24 158.7828 ~1.58 : 1/2 (kangle) 0.1012 221576.6904113.24 317.5656 ~1.9 : 1/2 (Kbond)(Kangle) How were these dielectric constants calculated? Did you collect sufficient data? It seems to me that there is no definitive dependence on any of these parameters, and you have one outlying point that is coincidentally close to what you want. A consistently wrong dielectric would suggest that either you're not calculating it right or you don't have sufficiently converged data. Based on a quick look through the paper, it seems to me that your original premise of converting between force fields is not related to the task at hand. Water models are relatively force field-agnostic, especially when trivial functional forms, such as harmonic potentials, are applied. There is nothing fancy here. Given the following: [ bondtypes ] ; ij func b0 kb OWHW 10.1012 443153.3808 ; J. Chem. Phys. (2006),124,024503 [ angletypes ] ; ijk func th0 cth HW OW HW 1 113.24 158.7828 ; J. Chem. Phys. (2006),124,024503 You are indeed applying simple harmonic potentials (see the manual to confirm the form), which again indicates to me that you should not be playing with the force constants in the model described in the paper. Use Ka and Kb as listed. Halving these quantities will result in a harmonic potential, e.g. for bonds of (1/4)Kb(b-b0)^2 rather then the proper coefficient of 1/2. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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 list
[gmx-users] git server maintenance finished
Hi, The git server, git.gromacs.org, was moved to a new machine: tcbs03.theophys.kth.se, 130.237.25.132. It may take some time for the DNS to propagate. The old server is still available at git-old.gromacs.org, 130.237.25.210. We'll take it offline after we make sure the new one runs fine. Cheers, Rossen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Fwd: Compiling issue : Compiling gromacs 4.5.4 with intel compiler suite 12.0
Hi, I recompiled gromacs 4.5.4 and fftw3.2.2 with the newest version off the intel compiler suit 12.0.2, still leading to segmentation faults. As suggested, I tried lots of combinations of different forcefields, water types and *.pdb's. Non of them was successful, so my segmentation fault is reproducible. Even the delivered tutorial/test cases stopped with a segmentation fault. As a last step, I will try to compile gromacs with CMake. If there are any alternatives you would suggest me to conduct, don't hesitated to let me know. Cheers, M.Kalavera -- NEU: FreePhone - kostenlos mobil telefonieren und surfen! Jetzt informieren: http://www.gmx.net/de/go/freephone -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Fatal error: Atomtype CB not found
Dear Sir Greetings! I am following every gromacs applications based on your manuals. I now get stuck in grompp -energy minimization step during generation of .tpr file for my ligand and protein. the error which i found is the following, Ignoring obsolete mdp entry 'title' Ignoring obsolete mdp entry 'cpp' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.5# WARNING 1 [file em.mdp, line unknown]: Unknown or double left-hand 'coulomtype' in parameter file checking input for internal consistency... processing topology... Opening library file /usr/share/gromacs/top/ ffG43a1.itp Opening library file /usr/share/gromacs/top/ffG43a1nb.itp Opening library file /usr/share/gromacs/top/ffG43a1bon.itp Opening library file /usr/share/gromacs/top/ff_dum.itp Generated 279 of the 1225 non-bonded parameter combinations --- Program grompp, VERSION 4.0.7 Source code file: ../../../../src/kernel/toppush.c, line: 947 Fatal error: Atomtype CB not found --- Sir, I couldn't understand what did it refers to? So I kindly request you spare your little time from your busy schedule to solve this problem. Thank you, Sir -- ** Ithayaraja M, Research Scholar, Department of Bionformatics, Bharathiar University, Coimbatore 641 046, Tamil Nadu India -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Fatal error: Atomtype CB not found
ITHAYARAJA wrote: Dear Sir Greetings! I am following every gromacs applications based on your manuals. I now get stuck in grompp -energy minimization step during generation of .tpr file for my ligand and protein. the error which i found is the following, Ignoring obsolete mdp entry 'title' Ignoring obsolete mdp entry 'cpp' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.5# WARNING 1 [file em.mdp, line unknown]: Unknown or double left-hand 'coulomtype' in parameter file checking input for internal consistency... processing topology... Opening library file /usr/share/gromacs/top/ ffG43a1.itp Opening library file /usr/share/gromacs/top/ffG43a1nb.itp Opening library file /usr/share/gromacs/top/ffG43a1bon.itp Opening library file /usr/share/gromacs/top/ff_dum.itp Generated 279 of the 1225 non-bonded parameter combinations --- Program grompp, VERSION 4.0.7 Source code file: ../../../../src/kernel/toppush.c, line: 947 Fatal error: Atomtype CB not found --- Sir, I couldn't understand what did it refers to? So I kindly request you spare your little time from your busy schedule to solve this problem. You're mixing and matching force fields. Atom type CB does not exist in Gromos96 43A1, it comes from the deprecated ffgmx force field. -Justin Thank you, Sir -- ** Ithayaraja M, Research Scholar, Department of Bionformatics, Bharathiar University, Coimbatore 641 046, Tamil Nadu India -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] tip4p.itp
Does anybody know the reference for TIP4P water, which is supplied in tip4p.itp in the /share folder, please? -- Dr. Vitaly V. Chaban, Department of Chemistry University of Rochester, Rochester, New York 14627-0216 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] tip4p.itp
On 2011-05-09 20.19, Vitaly Chaban wrote:
Does anybody know the reference for TIP4P water, which is supplied
in tip4p.itp in the /share folder, please?
--
Dr. Vitaly V. Chaban, Department of Chemistry
University of Rochester, Rochester, New York 14627-0216
Do you think it is not the regular one?
@Article{ Jorgensen83,
author = W. L. Jorgensen and J. Chandrasekhar and
J. D. Madura and R. W. Impey and M. L. Klein,
title =Comparison of simple potential functions for
simulating liquid water,
journal = J. Chem. Phys.,
year = 1983,
volume = 79,
pages =926--935
}
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] tip4p.itp
Vitaly Chaban wrote: Does anybody know the reference for TIP4P water, which is supplied in tip4p.itp in the /share folder, please? Reference 96 in the manual. -Justin -- Dr. Vitaly V. Chaban, Department of Chemistry University of Rochester, Rochester, New York 14627-0216 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: git server maintenance finished
The DNS seems to be finished updating now. Let me know if something doesn't work as expected with the new server. Cheers, Rossen On 5/9/11 5:25 PM, Rossen Apostolov wrote: Hi, The git server, git.gromacs.org, was moved to a new machine: tcbs03.theophys.kth.se, 130.237.25.132. It may take some time for the DNS to propagate. The old server is still available at git-old.gromacs.org, 130.237.25.210. We'll take it offline after we make sure the new one runs fine. Cheers, Rossen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Re: tip4p.itp
On 2011-05-09 20.19, Vitaly Chaban wrote:
Does anybody know the reference for TIP4P water, which is supplied
in tip4p.itp in the /share folder, please?
--
Dr. Vitaly V. Chaban, Department of Chemistry
University of Rochester, Rochester, New York 14627-0216
Do you think it is not the regular one?
@Article{ Jorgensen83,
author = W. L. Jorgensen and J. Chandrasekhar and
J. D. Madura and R. W. Impey and M. L. Klein,
title = Comparison of simple potential functions for
simulating liquid water,
journal = J. Chem. Phys.,
year = 1983,
volume = 79,
pages = 926--935
}
Thanks, everyone. I was just recently said about the novel revisions
of the TIP4P model, so I am anxious to provide a correct reference in
the article.
Vitaly
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] writing trajectory with water molecules within a distance from protein
Hi, there is no tool to do that. Trajectories assume to have the same number of atoms per frame. What you can do is use g_order (it gives you the water sorted by distance and the number of water within .5nm) or g_select (it can give you an index file with the atoms within .5nm for each frame) Roland On Mon, May 9, 2011 at 10:50 AM, maria goranovic mariagorano...@gmail.comwrote: Dear experts I have a protein simulation in a water box. I now want to write a trajectory containing only the protein, and water molecules within 5 Angstroms of the protein, with the water list being updated each time step. How can one do this? Appreciate the help -- Maria G. Technical University of Denmark Copenhagen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Res: [gmx-users] different number of waters (grompp)
Ricardo O. S. Soares wrote: Hello dear users, I'm having a problem trying to simulate one trimer. I'm using tip4p water and right after I fill the box with water and try to pre-process (grompp) the resulting .gro and .top, I get the following error: --- Program grompp, VERSION 4.5.1 Source code file: grompp.c, line: 377 Fatal error: number of coordinates in coordinate file (../box/box_water.gro, 274045) does not match topology (../top_water.top, 273029) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Here's the ending of the .top file: [ molecules ] ; Compound#mols Protein_chain_A 1 Protein_chain_H 1 Protein_chain_L 1 SOL59 SOL97 SOL98 SOL 66032 And the beginning of the .gro file shows the number 274045 The .top specifies fewer atoms than the .gro, so it's possible that there was some problem when genbox wrote the topology. The screen output of genbox should have indicated how many waters were added - does this number match what you see in the .top? Presumably the first three SOL entries are crystal waters? I don't know that pre-existing waters should cause any problem, but it's possible. The difference in the number of atoms is 1016, or 254 TIP4P molecules. Before updating to 4.5.4, I removed the crystal waters from the pdb file and now the grompp went fine. The problem was probably the different water notations after the genbox step. Here follows an exemple: Crystal water before (original pdb): ... HETATM 3999 O HOH A 410 24.263 -7.517 -15.541 1.00 27.99 O HETATM 4000 O HOH A 411 5.6827.359 2.277 1.00 35.66 O HETATM 4001 O HOH A 412 20.924 0.175 -18.311 1.00 30.25 O HETATM 4002 O HOH A 413 7.366 3.959 -6.173 1.00 36.77 O HETATM 4003 O HOH A 414 0.563 16.043 -5.418 1.00 29.62 O ... and the added tip4p waters: ... 121SOL OW 1760 0.519 0.692 0.680 121SOLHW1 1761 0.504 0.612 0.731 121SOLHW2 1762 0.601 0.727 0.714 121SOL MW 1763 0.527 0.684 0.692 122SOL OW 1764 0.856 1.378 1.365 ... I just wonder if the romoval of these crystal water may introduce artifacts to the simulation. Thanks for your insights! Coincidentally, 59 + 97 + 98 = 254. It looks like genbox wrote the wrong number of molecules it added. If this is the case, please file an issue on redmine.gromacs.org with the exact steps taken to reproduce the problem so it can be fixed. -Justin Thanks for your time. Ricardo. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Fwd: Compiling issue : Compiling gromacs 4.5.4 with intel compiler suite 12.0
On 10/05/2011 1:38 AM, kalav...@gmx.net wrote: Hi, I recompiled gromacs 4.5.4 and fftw3.2.2 with the newest version off the intel compiler suit 12.0.2, still leading to segmentation faults. As suggested, I tried lots of combinations of different forcefields, water types and *.pdb's. Non of them was successful, so my segmentation fault is reproducible. Even the delivered tutorial/test cases stopped with a segmentation fault. As a last step, I will try to compile gromacs with CMake. If there are any alternatives you would suggest me to conduct, don't hesitated to let me know. I would --disable-shared everything and see how things went. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Fatal error: Atomtype CB not found
On 10/05/2011 3:10 AM, Justin A. Lemkul wrote: ITHAYARAJA wrote: Dear Sir Greetings! I am following every gromacs applications based on your manuals. I now get stuck in grompp -energy minimization step during generation of .tpr file for my ligand and protein. the error which i found is the following, Ignoring obsolete mdp entry 'title' Ignoring obsolete mdp entry 'cpp' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.5# WARNING 1 [file em.mdp, line unknown]: Unknown or double left-hand 'coulomtype' in parameter file Spelling is particularly important when dealing with literal-minded computers. You have to get it right. Mark checking input for internal consistency... processing topology... Opening library file /usr/share/gromacs/top/ ffG43a1.itp Opening library file /usr/share/gromacs/top/ffG43a1nb.itp Opening library file /usr/share/gromacs/top/ffG43a1bon.itp Opening library file /usr/share/gromacs/top/ff_dum.itp Generated 279 of the 1225 non-bonded parameter combinations --- Program grompp, VERSION 4.0.7 Source code file: ../../../../src/kernel/toppush.c, line: 947 Fatal error: Atomtype CB not found --- Sir, I couldn't understand what did it refers to? So I kindly request you spare your little time from your busy schedule to solve this problem. You're mixing and matching force fields. Atom type CB does not exist in Gromos96 43A1, it comes from the deprecated ffgmx force field. -Justin Thank you, Sir -- ** Ithayaraja M, Research Scholar, Department of Bionformatics, Bharathiar University, Coimbatore 641 046, Tamil Nadu India -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] writing trajectory with water molecules within a distance from protein
On 10/05/2011 12:50 AM, maria goranovic wrote: Dear experts I have a protein simulation in a water box. I now want to write a trajectory containing only the protein, and water molecules within 5 Angstroms of the protein, with the water list being updated each time step. How can one do this? Appreciate the help g_select is useful for dynamic selections of this type. g_select -select help can give examples and such. I'd hope it's been designed so that then using trjconv to extract such selections works, but I can't think how, having not ever tried. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] total force acting on group
On 10/05/2011 12:43 AM, rasool.fakh...@ut.ac.ir wrote: Hi dear user's I want to calculate total force acting on one certain atom or group. gromacs dose not have tools for force analysis, and FDA only give pair forces between one group of atoms how can i do this? nstfout = xx in your .mdp file writes the MD forces to the .trr file. g_traj will then dump them to a text file. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] regarding nacl simulation in water using tabulated potentials
On 10/05/2011 2:20 AM, sreelakshmi ramesh wrote: i had three tables one for solvent na and solvent cl ions (obeying lj potential) and na ,cl obeying my own potential.i have the following mdp file em.mdp title = nacl cpp = /usr/bin/cpp ; the c preprocessor define= -DEFLEXIBLE integrator = md dt = 0.001 ; ps ! nsteps = 6 nstlist = -1 ns_type = grid rlist = 1.4 coulombtype = user rcoulomb = 1.0 energygrps = Na Cl Sol energygrp_table = Na Cl Na Sol Cl Sol If your mdrun -table file will be for LJ, then the only tables you need to specify here are for Na-Cl interactions. rvdw = 1.0 vdwtype= user fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 pbc=xyz; ; Energy minimizing stuff emtol = 1000.0 emstep = 0.01 *and topology file is as follows* [ defaults ] ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 11 yes 0.5 0.8333 [ atomtypes ] ; name bond type mass charge ptype C A NaNa 22.99 1 A 1.0e-03 ClCl 35.453-1 A 9.0e-06 [ nonbond params ] ;i j func A B C Na Cl 1 2.01E-09 3.154 11.2E-12 (buckingham) I dont have idea how to include water topology and include A B paramaters for water-ion interaction (lennard jones) Set up a normal aqueous Na Cl simulation and adapt that. Consult tutorial material for examples for including water. See http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials, like I suggested you search for earlier... Mark any help appreciated, sree lakshmi On Mon, May 9, 2011 at 12:37 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 9/05/2011 4:01 PM, sreelakshmi ramesh wrote: i had followed the instructions in themnaual for ninbonded interactions adn had created two tables one for nacl adn other table for water ion interations... That's not I really don't have any idea on how to do this. Please ask the question you want answered, or you're wasting everyone's time. i wanted some information on how to use these tables for starting thee simulation Sorry, that's too general. You might want help with a command line, or setting up the .mdp, or something else. Please read 6.7 of the manual, try things, and ask a focused question. Mark On Mon, May 9, 2011 at 11:20 AM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 9/05/2011 3:46 PM, sreelakshmi ramesh wrote: dear gmx users, i have to simulate nacl in water...the system is acubic box with just one na adn one cl ion in tip3p water.i wanted to use a buckingham potential for na adn cl interaction and lennard jones for water -ion intercation.i really dont have any idea on how to do this.any help will be of great use for me... Can't be done simply. You'd have to use non-bonded interaction tables for the Na-Cl interaction with properly constructed energy groups. Search the manual and webpage for details. Mark -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
