Re: [gmx-users] Re: Peptide folding simulation
Hi, Check this article: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0032131 HTH Balazs Quoting simula_460 bharat.85.m...@gmail.com: Hi, I tried again simulating the same peptide with OPLS FF for 2000 ns time duration. I used VMD for the secondary structure analysis and trajectory visualization. This time I was able to get folding events but the residues that are should be beta strands were helical for most of the time during simulation. Is it because of the parameters or what else could have gone wrong ?? BHARAT -- View this message in context: http://gromacs.5086.n6.nabble.com/Peptide-folding-simulation-tp4999215p4999506.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 * Only plain text messages are allowed! * 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 with Inflategro!!!
Thanks for the message, I have a .pdb containing my membrane protein inside the leaflet of popc bilayer, so i wanted to remove the interacting lipid molecules, hence i used inflategro. I used CHARMM GUI only to produce a pure POPC bilayer, I didnt produce a protein bilayer system using that, because I wanted to fix/orient my protein exactly according to my need, so I was using SYBYL to do it. the box vector values were 11.13710 11.41790 7.60370 and after changing HOH to SOL, my water molecules disappeared as expected. On Tue, Jul 17, 2012 at 12:03 AM, Justin Lemkul jalem...@vt.edu wrote: On 7/16/12 5:42 PM, Manikam Sadasivam Saravanan wrote: Hi, I am a new user to Gromacs, just started exploring it since 3 months, Thanks to Justin, In-fact i learned a lot form his tutorial using KALP protein in dppc. Currently I am working with simulation of Membrane protein in a popc bilayer, its a complete membrane protien which lies in one of the leaflet of the bilayer. I placed my protein inside the popc bilayer (developed using Charmm GUI) in the exact position using SYBYL , same as what is done in the building unit cell part of the KALP tutorial and with the satisfied orientation of protein. Then the final pdb with protein, popc and water molecules is used to produce a .gro file using pdb2gmx tool. later I tried to do Inflategro to remove the unwanted lipid molecules interacting with my protein, but i was not successful because, when i visualize my .gro file of system-inflated, my water molecules are still present and my protein is out of from my lipid box and when i shrink the bilayer, the protein is completely lost! could you please give me an idea to do a proper inflated and deflate in my case? thank you!! Why do you even need InflateGRO? Is there some reason CHARMM-GUI produces an unsatisfactory result? I thought that it could produce membrane protein systems, in which case you don't need to do anything. Unfortunately, at this point, it's impossible to know what's going wrong. There are too many weird things going on, none of which should be happening with a sensible input. A few things to consider: 1. What are the box vectors in the .gro file produced by pdb2gmx? 2. Are the water molecules named properly? InflateGRO expects them to be named SOL in order to work. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * 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 -- MSS -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] problems with pdb2gmx
Hi everybody, I want to use pdb2gmx for my protein. My protein has a ACE cap at one termini. And I looked it up in the aminoacids.rtp file and there is also a ACE entry. But still I get an error when using pdb2gmx my command is like this: pdb2gmx -f 3m71_hyd_cap.pdb -o 3m71.gro -p 3m71.top -ter -lys -arg -asp -glu -his -water tip3p -ff amber03 I use it this why because I want to the residues to be protonated (-lys -arg -asp -glu -his) and the termini shell be not charged (-ter) My error is: Atom HH1 in residue ACE 5 was not found in rtp entry ACE with 6 atoms while sorting atoms. I understand that there is a different between my ACE definition and the one form gromacs. The ACE in my file look like this: ATOM 1 CH3 ACE 5 -15.187 -10.824 -17.012 1.00 0.00 C ATOM 2 C ACE 5 -15.919 -10.927 -15.673 1.00 0.00 C ATOM 3 O ACE 5 -15.898 -9.978 -14.893 1.00 0.00 O ATOM 4 1H ACE 5 -14.703 -9.826 -17.094 1.00 0.00 H ATOM 5 2H ACE 5 -14.413 -11.621 -17.076 1.00 0.00 H ATOM 6 3H ACE 5 -15.914 -10.956 -17.845 1.00 0.00 H And the definition in gromacs looks like this: [ ACE ] [ atoms ] HH31HC 0.0760101 CH3CT -0.1902642 HH32HC 0.0760113 HH33HC 0.0760104 CC0.5124035 OO -0.5501706 [ bonds ] HH31 CH3 CH3 HH32 CH3 HH33 CH3 C C O [ impropers ] CH3+N C O The differ in the names of the hydrogen atoms. So what can I do now that they are the same? I already tried to name the ones in my pdb file like the ones in the rtp file (HH33 instead of 3H). And I tried to name the hydrogens in the rtp file like the ones in pdb file (H1 instead of HH31). But nothing worked. Thank you for your help!! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 with Inflategro!!!
On 7/18/12 5:57 AM, Manikam Sadasivam Saravanan wrote: Thanks for the message, I have a .pdb containing my membrane protein inside the leaflet of popc bilayer, so i wanted to remove the interacting lipid molecules, hence i used inflategro. I used CHARMM GUI only to produce a pure POPC bilayer, I didnt produce a protein bilayer system using that, because I wanted to fix/orient my protein exactly according to my need, so I was using SYBYL to do it. the box vector values were 11.13710 11.41790 7.60370 and after changing HOH to SOL, my water molecules disappeared as expected. So is the problem solved then? -Justin On Tue, Jul 17, 2012 at 12:03 AM, Justin Lemkul jalem...@vt.edu wrote: On 7/16/12 5:42 PM, Manikam Sadasivam Saravanan wrote: Hi, I am a new user to Gromacs, just started exploring it since 3 months, Thanks to Justin, In-fact i learned a lot form his tutorial using KALP protein in dppc. Currently I am working with simulation of Membrane protein in a popc bilayer, its a complete membrane protien which lies in one of the leaflet of the bilayer. I placed my protein inside the popc bilayer (developed using Charmm GUI) in the exact position using SYBYL , same as what is done in the building unit cell part of the KALP tutorial and with the satisfied orientation of protein. Then the final pdb with protein, popc and water molecules is used to produce a .gro file using pdb2gmx tool. later I tried to do Inflategro to remove the unwanted lipid molecules interacting with my protein, but i was not successful because, when i visualize my .gro file of system-inflated, my water molecules are still present and my protein is out of from my lipid box and when i shrink the bilayer, the protein is completely lost! could you please give me an idea to do a proper inflated and deflate in my case? thank you!! Why do you even need InflateGRO? Is there some reason CHARMM-GUI produces an unsatisfactory result? I thought that it could produce membrane protein systems, in which case you don't need to do anything. Unfortunately, at this point, it's impossible to know what's going wrong. There are too many weird things going on, none of which should be happening with a sensible input. A few things to consider: 1. What are the box vectors in the .gro file produced by pdb2gmx? 2. Are the water molecules named properly? InflateGRO expects them to be named SOL in order to work. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * 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. Research Scientist 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 * Only plain text messages are allowed! * 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] problems with pdb2gmx
On 18/07/2012 7:58 PM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, I want to use pdb2gmx for my protein. My protein has a ACE cap at one termini. And I looked it up in the aminoacids.rtp file and there is also a ACE entry. But still I get an error when using pdb2gmx my command is like this: pdb2gmx -f 3m71_hyd_cap.pdb -o 3m71.gro -p 3m71.top -ter -lys -arg -asp -glu -his -water tip3p -ff amber03 I use it this why because I want to the residues to be protonated (-lys -arg -asp -glu -his) and the termini shell be not charged (-ter) More particularly, you want no N terminus, since you are supplying it yourself. This may be the origin of your problem. My error is: Atom HH1 in residue ACE 5 was not found in rtp entry ACE with 6 atoms while sorting atoms. I understand that there is a different between my ACE definition and the one form gromacs. The ACE in my file look like this: ATOM 1 CH3 ACE 5 -15.187 -10.824 -17.012 1.00 0.00 C ATOM 2 C ACE 5 -15.919 -10.927 -15.673 1.00 0.00 C ATOM 3 O ACE 5 -15.898 -9.978 -14.893 1.00 0.00 O ATOM 4 1H ACE 5 -14.703 -9.826 -17.094 1.00 0.00 H ATOM 5 2H ACE 5 -14.413 -11.621 -17.076 1.00 0.00 H ATOM 6 3H ACE 5 -15.914 -10.956 -17.845 1.00 0.00 H You can try hydrogen names like HH1 if the above doesn't work, but I believe GROMACS is trying to follow orders and use neutral termini. Reading and/or including the last fragment of the pdb2gmx output in your email would have been instructive. You also need to get your C-terminus residue naming correct... e.g. CGLY for glycine. Mark And the definition in gromacs looks like this: [ ACE ] [ atoms ] HH31HC 0.0760101 CH3CT -0.1902642 HH32HC 0.0760113 HH33HC 0.0760104 CC0.5124035 OO -0.5501706 [ bonds ] HH31 CH3 CH3 HH32 CH3 HH33 CH3 C C O [ impropers ] CH3+N C O The differ in the names of the hydrogen atoms. So what can I do now that they are the same? I already tried to name the ones in my pdb file like the ones in the rtp file (HH33 instead of 3H). And I tried to name the hydrogens in the rtp file like the ones in pdb file (H1 instead of HH31). But nothing worked. Thank you for your help!! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] problems with pdb2gmx
On 7/18/12 5:58 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, I want to use pdb2gmx for my protein. My protein has a ACE cap at one termini. And I looked it up in the aminoacids.rtp file and there is also a ACE entry. But still I get an error when using pdb2gmx my command is like this: pdb2gmx -f 3m71_hyd_cap.pdb -o 3m71.gro -p 3m71.top -ter -lys -arg -asp -glu -his -water tip3p -ff amber03 I use it this why because I want to the residues to be protonated (-lys -arg -asp -glu -his) and the termini shell be not charged (-ter) My error is: Atom HH1 in residue ACE 5 was not found in rtp entry ACE with 6 atoms while sorting atoms. I understand that there is a different between my ACE definition and the one form gromacs. The ACE in my file look like this: ATOM 1 CH3 ACE 5 -15.187 -10.824 -17.012 1.00 0.00 C ATOM 2 C ACE 5 -15.919 -10.927 -15.673 1.00 0.00 C ATOM 3 O ACE 5 -15.898 -9.978 -14.893 1.00 0.00 O ATOM 4 1H ACE 5 -14.703 -9.826 -17.094 1.00 0.00 H ATOM 5 2H ACE 5 -14.413 -11.621 -17.076 1.00 0.00 H ATOM 6 3H ACE 5 -15.914 -10.956 -17.845 1.00 0.00 H And the definition in gromacs looks like this: [ ACE ] [ atoms ] HH31HC 0.0760101 CH3CT -0.1902642 HH32HC 0.0760113 HH33HC 0.0760104 CC0.5124035 OO -0.5501706 [ bonds ] HH31 CH3 CH3 HH32 CH3 HH33 CH3 C C O [ impropers ] CH3+N C O The differ in the names of the hydrogen atoms. So what can I do now that they are the same? I already tried to name the ones in my pdb file like the ones in the rtp file (HH33 instead of 3H). And I tried to name the hydrogens in the rtp file like the ones in pdb file (H1 instead of HH31). But nothing worked. Use -ignh and pdb2gmx will rebuild all hydrogens for you. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Peptide folding simulation
On 7/18/12 3:03 AM, joja...@jgypk.u-szeged.hu wrote: Hi, Check this article: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0032131 HTH Balazs In addition, it is important to realize that a single trajectory represents one possible outcome, and no matter how long it is, may be stuck in a local energy minimum. In general, multiple simulations of intermediate length are often considered better than one long trajectory. In addition, enhanced sampling methods like REMD are used very frequently in studies on protein folding so that energy barriers are more easily overcome. -Justin Quoting simula_460 bharat.85.m...@gmail.com: Hi, I tried again simulating the same peptide with OPLS FF for 2000 ns time duration. I used VMD for the secondary structure analysis and trajectory visualization. This time I was able to get folding events but the residues that are should be beta strands were helical for most of the time during simulation. Is it because of the parameters or what else could have gone wrong ?? BHARAT -- View this message in context: http://gromacs.5086.n6.nabble.com/Peptide-folding-simulation-tp4999215p4999506.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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. Research Scientist 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 * Only plain text messages are allowed! * 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] Gromacs/Orca coordinates error
Dear gmx users, I am running a QM/MM optimization using the interface with Orca and the bOPT=Yes option. I departed from a snapshot taken from a MM molecular dynamics simulation. The calculation starts running well, and the QM part converges successfully after 29 optimization cycles. However, at this point, and after printing OPTIMIZATION RUN DONE in the Orca output, I get the next error: Error: number expected in COORDS/FirstCoordinate ATOM-NO 2 And looking at the Orca input, I see that the coordinates of some atoms are not properly printed out and instead nan is written. So, I do not if the error is due to a bad initial geometry (but then I expect a converge error) or there is something I am missing. Any help will be appreciated. Jon -- View this message in context: http://gromacs.5086.n6.nabble.com/Gromacs-Orca-coordinates-error-tp4999517.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] How to compute the C-H bond time correlation function for surfactant alkyl chain in micelle with the CHARMM and GROMOS
Hi All, I would like to compute the time correlation function (tcf) of the C-H bond vector for all the C-H bonds on the hydrocarbon chain of surfactants in two micelles simulated with the CHARMM and gromos54A7 force fields. It is not clear to me how do that. Below what i did 1- For the CHARMM simulation I have constructed an index file that contains all the C H atoms of the alkyl chain, like this : aC12 | aH12A | aH12B aC13 | aH13A | aH13B ... ... ... up to the last methylene group aC23| aH23A | aH23B It is Correct ? 2- And use the following command for example for the C12-H bond vector g_rotacf_mpi -f micelle_Center_All.xtc -s run_1.tpr -b 11 -e 13 -fitfn aexp -d -n micelle_CH_Bonds.ndx -o micelle_rotacf-C12-P2.xvg bond_C12.txt It is also Correct ? I have indeed obtained a correlation function C(t), that i can fit with 4 exponential but i am not sure if this function is what i expect. IF It is ok, i would like to do the same calculations for surfactants simulated with GROMOS force field. Since in this force field the apolar hydrogens are not presents, i need to reconstruct them from hydrocarbon chain backbone. Again how to do that ? Your guidance would be helpful for me. Best SA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 with Inflategro!!!
no, water problem is solved, but my protein is still out of the bilayer, When i change:minimize my box vector values and inflate...the protein is packed inside. but now the area per lipid is too low for popc its like 0.148 nm2 On Wed, Jul 18, 2012 at 12:08 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/18/12 5:57 AM, Manikam Sadasivam Saravanan wrote: Thanks for the message, I have a .pdb containing my membrane protein inside the leaflet of popc bilayer, so i wanted to remove the interacting lipid molecules, hence i used inflategro. I used CHARMM GUI only to produce a pure POPC bilayer, I didnt produce a protein bilayer system using that, because I wanted to fix/orient my protein exactly according to my need, so I was using SYBYL to do it. the box vector values were 11.13710 11.41790 7.60370 and after changing HOH to SOL, my water molecules disappeared as expected. So is the problem solved then? -Justin On Tue, Jul 17, 2012 at 12:03 AM, Justin Lemkul jalem...@vt.edu wrote: On 7/16/12 5:42 PM, Manikam Sadasivam Saravanan wrote: Hi, I am a new user to Gromacs, just started exploring it since 3 months, Thanks to Justin, In-fact i learned a lot form his tutorial using KALP protein in dppc. Currently I am working with simulation of Membrane protein in a popc bilayer, its a complete membrane protien which lies in one of the leaflet of the bilayer. I placed my protein inside the popc bilayer (developed using Charmm GUI) in the exact position using SYBYL , same as what is done in the building unit cell part of the KALP tutorial and with the satisfied orientation of protein. Then the final pdb with protein, popc and water molecules is used to produce a .gro file using pdb2gmx tool. later I tried to do Inflategro to remove the unwanted lipid molecules interacting with my protein, but i was not successful because, when i visualize my .gro file of system-inflated, my water molecules are still present and my protein is out of from my lipid box and when i shrink the bilayer, the protein is completely lost! could you please give me an idea to do a proper inflated and deflate in my case? thank you!! Why do you even need InflateGRO? Is there some reason CHARMM-GUI produces an unsatisfactory result? I thought that it could produce membrane protein systems, in which case you don't need to do anything. Unfortunately, at this point, it's impossible to know what's going wrong. There are too many weird things going on, none of which should be happening with a sensible input. A few things to consider: 1. What are the box vectors in the .gro file produced by pdb2gmx? 2. Are the water molecules named properly? InflateGRO expects them to be named SOL in order to work. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * 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. Research Scientist 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 * Only plain text messages are allowed! * 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 -- MSS -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 with Inflategro!!!
On 7/18/12 7:07 AM, Manikam Sadasivam Saravanan wrote: no, water problem is solved, but my protein is still out of the bilayer, When i change:minimize my box vector values and inflate...the protein What does this mean? is packed inside. but now the area per lipid is too low for popc its like 0.148 nm2 After inflation, the area should be huge. What was your command line for InflateGRO? If the protein is not in the desired location, you need to use editconf -center to adjust its coordinates. Make sure it is also within a box that matches that of the lipid bilayer. -Justin On Wed, Jul 18, 2012 at 12:08 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/18/12 5:57 AM, Manikam Sadasivam Saravanan wrote: Thanks for the message, I have a .pdb containing my membrane protein inside the leaflet of popc bilayer, so i wanted to remove the interacting lipid molecules, hence i used inflategro. I used CHARMM GUI only to produce a pure POPC bilayer, I didnt produce a protein bilayer system using that, because I wanted to fix/orient my protein exactly according to my need, so I was using SYBYL to do it. the box vector values were 11.13710 11.41790 7.60370 and after changing HOH to SOL, my water molecules disappeared as expected. So is the problem solved then? -Justin On Tue, Jul 17, 2012 at 12:03 AM, Justin Lemkul jalem...@vt.edu wrote: On 7/16/12 5:42 PM, Manikam Sadasivam Saravanan wrote: Hi, I am a new user to Gromacs, just started exploring it since 3 months, Thanks to Justin, In-fact i learned a lot form his tutorial using KALP protein in dppc. Currently I am working with simulation of Membrane protein in a popc bilayer, its a complete membrane protien which lies in one of the leaflet of the bilayer. I placed my protein inside the popc bilayer (developed using Charmm GUI) in the exact position using SYBYL , same as what is done in the building unit cell part of the KALP tutorial and with the satisfied orientation of protein. Then the final pdb with protein, popc and water molecules is used to produce a .gro file using pdb2gmx tool. later I tried to do Inflategro to remove the unwanted lipid molecules interacting with my protein, but i was not successful because, when i visualize my .gro file of system-inflated, my water molecules are still present and my protein is out of from my lipid box and when i shrink the bilayer, the protein is completely lost! could you please give me an idea to do a proper inflated and deflate in my case? thank you!! Why do you even need InflateGRO? Is there some reason CHARMM-GUI produces an unsatisfactory result? I thought that it could produce membrane protein systems, in which case you don't need to do anything. Unfortunately, at this point, it's impossible to know what's going wrong. There are too many weird things going on, none of which should be happening with a sensible input. A few things to consider: 1. What are the box vectors in the .gro file produced by pdb2gmx? 2. Are the water molecules named properly? InflateGRO expects them to be named SOL in order to work. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * 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. Research Scientist 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 * Only plain text messages are allowed! * 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. Research Scientist 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 * Only plain text messages are allowed! * Please search the
[gmx-users] Merging of two trajectories
Dear Gromacs Users! I have two trajectories with removed PBC which was done by the below command. trjconv -s MD_B2ar_WP_3.tpr -f MD_B2ar_WP_3.trr -o md_noPBC.xtc -pbc mol -ur compact Both of that trajectories are of the same system- when one trajectory have been manyally stoped I've run the second one from the end of the first trajectory using cpt file of the first simulation. I have no problem with that data but when I try to merge it by means of VMD and obtain the whole file I noticed that new trajectory consist of wrong kinetik data. E.g on the RMSD or some other graph the TIME values are always incorrect. How I could prevent this and obtain correct whole trajectory file from 2 or more parts? Thanks for help James -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Merging of two trajectories
On 7/18/12 7:35 AM, James Starlight wrote: Dear Gromacs Users! I have two trajectories with removed PBC which was done by the below command. trjconv -s MD_B2ar_WP_3.tpr -f MD_B2ar_WP_3.trr -o md_noPBC.xtc -pbc mol -ur compact Both of that trajectories are of the same system- when one trajectory have been manyally stoped I've run the second one from the end of the first trajectory using cpt file of the first simulation. I have no problem with that data but when I try to merge it by means of VMD and obtain the whole file I noticed that new trajectory consist of wrong kinetik data. E.g on the RMSD or some other graph the TIME values are always incorrect. How I could prevent this and obtain correct whole trajectory file from 2 or more parts? Use trjcat to concatenate the trajectories. The -settime option will allow you to fix any potential issues with timestep, though if the simulations were all run with Gromacs and continued via .cpt file, there should be no need. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * 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 with Inflategro!!!
my command to inflate was - perl inflategro.pl protein_popc.gro 4 POPC 14 system_inflated.gro 5 area.dat my gro file looks like, membrane protein in POPC 121-310KWITNOIONS 59522 1SER N1 -2.092 -1.832 -1.359 1SERHT12 -2.149 -1.861 -1.436 1SERHT23 -2.150 -1.809 -1.281 1SER CA4 -2.002 -1.942 -1.322 ... 91ILEOT1 1527 0.033 1.945 -1.049 91ILEOT2 1528 0.057 1.922 -1.267 continued by popc and sol 1POPC N1 2.963 -2.658 2.064 1POPC C122 3.003 -2.713 2.196 1POPC C133 2.954 -2.509 2.062 . 8764SOL OW57992 3.731 3.721 -2.405 8764SOLHW157993 3.749 3.653 -2.341 8764SOLHW257994 3.723 3.802 -2.353 11.13710 11.41790 7.60370 when I inflate with box vectors value 11.13710 11.41790 7.60370, my protein is out of inflated lipid boundary. if i change my value to 1.39213 1.42723 0.0 (dividing above value by half and half), now my protein is at the center of inflated popc. but the area per lipid even after inflation is still only 0.148 nm2. should i use editconf with the whole .gro file containing protein, popc or i have to separate my protein only as a new.gro file and perform editconf and then cat? thanks for the suggestions! On Wed, Jul 18, 2012 at 1:24 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/18/12 7:07 AM, Manikam Sadasivam Saravanan wrote: no, water problem is solved, but my protein is still out of the bilayer, When i change:minimize my box vector values and inflate...the protein What does this mean? is packed inside. but now the area per lipid is too low for popc its like 0.148 nm2 After inflation, the area should be huge. What was your command line for InflateGRO? If the protein is not in the desired location, you need to use editconf -center to adjust its coordinates. Make sure it is also within a box that matches that of the lipid bilayer. -Justin On Wed, Jul 18, 2012 at 12:08 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/18/12 5:57 AM, Manikam Sadasivam Saravanan wrote: Thanks for the message, I have a .pdb containing my membrane protein inside the leaflet of popc bilayer, so i wanted to remove the interacting lipid molecules, hence i used inflategro. I used CHARMM GUI only to produce a pure POPC bilayer, I didnt produce a protein bilayer system using that, because I wanted to fix/orient my protein exactly according to my need, so I was using SYBYL to do it. the box vector values were 11.13710 11.41790 7.60370 and after changing HOH to SOL, my water molecules disappeared as expected. So is the problem solved then? -Justin On Tue, Jul 17, 2012 at 12:03 AM, Justin Lemkul jalem...@vt.edu wrote: On 7/16/12 5:42 PM, Manikam Sadasivam Saravanan wrote: Hi, I am a new user to Gromacs, just started exploring it since 3 months, Thanks to Justin, In-fact i learned a lot form his tutorial using KALP protein in dppc. Currently I am working with simulation of Membrane protein in a popc bilayer, its a complete membrane protien which lies in one of the leaflet of the bilayer. I placed my protein inside the popc bilayer (developed using Charmm GUI) in the exact position using SYBYL , same as what is done in the building unit cell part of the KALP tutorial and with the satisfied orientation of protein. Then the final pdb with protein, popc and water molecules is used to produce a .gro file using pdb2gmx tool. later I tried to do Inflategro to remove the unwanted lipid molecules interacting with my protein, but i was not successful because, when i visualize my .gro file of system-inflated, my water molecules are still present and my protein is out of from my lipid box and when i shrink the bilayer, the protein is completely lost! could you please give me an idea to do a proper inflated and deflate in my case? thank you!! Why do you even need InflateGRO? Is there some reason CHARMM-GUI produces an unsatisfactory result? I thought that it could produce membrane protein systems, in which case you don't need to do anything. Unfortunately, at this point, it's impossible to know what's going wrong. There are too many weird things going on, none of which should be happening with a sensible input. A few things to consider: 1. What are the box vectors in the .gro file produced by pdb2gmx? 2. Are the water molecules named properly? InflateGRO expects them to be named SOL in order to work. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain
Re: [gmx-users] Problem with Inflategro!!!
On 7/18/12 7:48 AM, Manikam Sadasivam Saravanan wrote: my command to inflate was - perl inflategro.pl protein_popc.gro 4 POPC 14 system_inflated.gro 5 area.dat my gro file looks like, membrane protein in POPC 121-310KWITNOIONS 59522 1SER N1 -2.092 -1.832 -1.359 1SERHT12 -2.149 -1.861 -1.436 1SERHT23 -2.150 -1.809 -1.281 1SER CA4 -2.002 -1.942 -1.322 ... 91ILEOT1 1527 0.033 1.945 -1.049 91ILEOT2 1528 0.057 1.922 -1.267 continued by popc and sol 1POPC N1 2.963 -2.658 2.064 1POPC C122 3.003 -2.713 2.196 1POPC C133 2.954 -2.509 2.062 . 8764SOL OW57992 3.731 3.721 -2.405 8764SOLHW157993 3.749 3.653 -2.341 8764SOLHW257994 3.723 3.802 -2.353 11.13710 11.41790 7.60370 when I inflate with box vectors value 11.13710 11.41790 7.60370, my protein is out of inflated lipid boundary. if i change my value to So these box vectors are the inflated ones, or the original? Not that it matters much, I'm just confused. 1.39213 1.42723 0.0 (dividing above value by half and half), You're doing more than dividing by half, and a zero length for the z-dimension is nonsensical. Do not manipulate the box vectors yourself. now my protein is at the center of inflated popc. but the area per lipid even after inflation is still only 0.148 nm2. The small area per lipid is a consequence of the massive reduction in the box size that your manual vectors impose. should i use editconf with the whole .gro file containing protein, popc or i have to separate my protein only as a new.gro file and perform editconf and then cat? When I build these systems, I do the following: 1. Note the box vectors in the bilayer coordinate file (don't modify them) 2. Position protein in a box with those same vectors and (if necessary) translate its coordinates using editconf -center or editconf -translate/-rotate as needed. 3. Concatenate the protein and bilayer coordinate files and adjust number of atoms accordingly. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * 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] Error reading .xtc file
Dear users, I am getting the problem in reading full .xtc file. The simulation time is 200 ns. But while giving command ./g_hbond -f dna_pro_whole_nojump_cent.xtc -s sys2.tpr -num Pro_H2A2.xvg I am getting below error. The .xtc file is reading only till 20ns and givng error. I am not getting error for other .xtc files Please provide soultion to the problem. * Calculating hydrogen bonds in Protein (12424 atoms) Found 1231 donors and 2226 acceptors Reading frame 0 time 0.000 Will do grid-seach on 29x20x30 grid, rcut=0.35 Reading frame 2000 time 2.000 --- Program g_hbond, VERSION 4.5.5 Source code file: gmx_hbond.c, line: 1211 Fatal error: Your computational box has shrunk too much. g_hbond can not handle this situation, sorry. * NIKHIL S. GADEWAL ACTREC, Tata Memorial Centre, Kharghar, Navi Mumbai, India -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Error reading .xtc file
On 7/18/12 8:24 AM, nikhil gadewal wrote: Dear users, I am getting the problem in reading full .xtc file. The simulation time is 200 ns. But while giving command ./g_hbond -f dna_pro_whole_nojump_cent.xtc -s sys2.tpr -num Pro_H2A2.xvg I am getting below error. The .xtc file is reading only till 20ns and givng error. I am not getting error for other .xtc files Please provide soultion to the problem. It sounds like you have massive changes to your box dimensions. Since g_hbond uses a grid-based search scheme to look for hydrogen bonds, such large changes cause the program to fail. Investigate the integrity of your .xtc file with gmxcheck and plot box vectors from the .edr file. Your system may have had serious problems at some point or the .xtc file became corrupted. -Justin * Calculating hydrogen bonds in Protein (12424 atoms) Found 1231 donors and 2226 acceptors Reading frame 0 time0.000 Will do grid-seach on 29x20x30 grid, rcut=0.35 Reading frame2000 time 2.000 --- Program g_hbond, VERSION 4.5.5 Source code file: gmx_hbond.c, line: 1211 Fatal error: Your computational box has shrunk too much. g_hbond can not handle this situation, sorry. * NIKHIL S. GADEWAL ACTREC, Tata Memorial Centre, Kharghar, Navi Mumbai, India -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * 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: About lipid simulation...
Hi Gromacs friends I read the Gromacs manual for 4.5.4, Section 3.4 page no 33, Surface tension coupling work with only Berendsen Press coupling. Please , would you tell me how to calculate lateral surface tension from P|| ( lateral press ) and Pz( Perpendicular press ) ??? ( Why to say P|| = -30 Pz = 1 , will give the teral tension of 20 mNm/m ???) I found out the way to calculate the lateral pressure.. As per the article ..Biophysics Journal, October 1995, vol 65, page no 1230. The formula as per article is Boundary lateral press = 1 - ( Surface Tension / Thickness in Z dimension.)... ; Temperature coupling is on tcoupl= Berendsen; More accurate thermostat tc-grps= Protein DPPCSOL_CL; three coupling groups - more accurate tau_t= 0.10.10.1; time constant, in ps ref_t= 323 323323; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl= Berendsen; Pressure coupling on in NPT vectors, independent z tau_p= 0.5; time constant, in ps ref_p= -30.01.0; reference pressure, x-y,z (in bar) compressibility = 5.0e-55.0e-5; isothermal compressibility, bar^-1 pcoupltype= What pcoupltype shouild be used ??? semiisotropic or Surface-tension Please give me the valuable suggestion in these regard Thank you in advance. Have a nice Day. With best wishes and regards, Rama David -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Merging of two trajectories
Justin thanks for advise I've used the bellow command for both trajectory trjcat -f md_noPBC.xtc md_noPBC_GO.xtc -tu ps -o merged_noPBC.xtc but resulted merged_noPBC.xtc consist of data from only second trajectory although in the log file both trajectories have been processed File Current start (ps) New start (ps) - md_noPBC.xtc0.000 ps 0 md_noPBC_GO.xtc0.000 ps 0 Summary of files and start times used: FileStart time Time step - md_noPBC.xtc0.000 ps7.000 ps md_noPBC_GO.xtc0.000 ps7.000 ps WARNING: same Start time as previous Back Off! I just backed up merged_noPBC.xtc to ./#merged_noPBC.xtc.5# Reading frame 0 time0.000 Reading frame3000 time 21000.000 Reading frame 0 time0.000 Continue writing frames from md_noPBC_GO.xtc t=0 ps, frame=0 Reading frame 1 time 7.000- frame 1 time 7.000 ps Last frame written was 10008, time 70056.00 ps Why this occurs ? By the way if I'm using -cat option resulted file consist of both trajectories ( in the separate enties). James 2012/7/18 Justin Lemkul jalem...@vt.edu: On 7/18/12 7:35 AM, James Starlight wrote: Dear Gromacs Users! I have two trajectories with removed PBC which was done by the below command. trjconv -s MD_B2ar_WP_3.tpr -f MD_B2ar_WP_3.trr -o md_noPBC.xtc -pbc mol -ur compact Both of that trajectories are of the same system- when one trajectory have been manyally stoped I've run the second one from the end of the first trajectory using cpt file of the first simulation. I have no problem with that data but when I try to merge it by means of VMD and obtain the whole file I noticed that new trajectory consist of wrong kinetik data. E.g on the RMSD or some other graph the TIME values are always incorrect. How I could prevent this and obtain correct whole trajectory file from 2 or more parts? Use trjcat to concatenate the trajectories. The -settime option will allow you to fix any potential issues with timestep, though if the simulations were all run with Gromacs and continued via .cpt file, there should be no need. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * 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 * Only plain text messages are allowed! * 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] Merging of two trajectories
On 7/18/12 9:34 AM, James Starlight wrote: Justin thanks for advise I've used the bellow command for both trajectory trjcat -f md_noPBC.xtc md_noPBC_GO.xtc -tu ps -o merged_noPBC.xtc but resulted merged_noPBC.xtc consist of data from only second trajectory although in the log file both trajectories have been processed File Current start (ps) New start (ps) - md_noPBC.xtc0.000 ps 0 md_noPBC_GO.xtc0.000 ps 0 Summary of files and start times used: FileStart time Time step - md_noPBC.xtc0.000 ps7.000 ps md_noPBC_GO.xtc0.000 ps7.000 ps WARNING: same Start time as previous Back Off! I just backed up merged_noPBC.xtc to ./#merged_noPBC.xtc.5# Reading frame 0 time0.000 Reading frame3000 time 21000.000 Reading frame 0 time0.000 Continue writing frames from md_noPBC_GO.xtc t=0 ps, frame=0 Reading frame 1 time 7.000- frame 1 time 7.000 ps Last frame written was 10008, time 70056.00 ps Why this occurs ? Because you're telling trjcat that both trajectories start at the same time, so they're going to overwrite one another. If they are indeed two separate segments of a continuous trajectory, they need different start times, one zero and one non-zero. By the way if I'm using -cat option resulted file consist of both trajectories ( in the separate enties). That's what -cat is designed to do. I doubt you want that in this case. The times will still be wrong. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * 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] Merging of two trajectories
Justin thanks, Works perfect. James 2012/7/18 Justin Lemkul jalem...@vt.edu: On 7/18/12 9:34 AM, James Starlight wrote: Justin thanks for advise I've used the bellow command for both trajectory trjcat -f md_noPBC.xtc md_noPBC_GO.xtc -tu ps -o merged_noPBC.xtc but resulted merged_noPBC.xtc consist of data from only second trajectory although in the log file both trajectories have been processed File Current start (ps) New start (ps) - md_noPBC.xtc0.000 ps 0 md_noPBC_GO.xtc0.000 ps 0 Summary of files and start times used: FileStart time Time step - md_noPBC.xtc0.000 ps7.000 ps md_noPBC_GO.xtc0.000 ps7.000 ps WARNING: same Start time as previous Back Off! I just backed up merged_noPBC.xtc to ./#merged_noPBC.xtc.5# Reading frame 0 time0.000 Reading frame3000 time 21000.000 Reading frame 0 time0.000 Continue writing frames from md_noPBC_GO.xtc t=0 ps, frame=0 Reading frame 1 time 7.000- frame 1 time 7.000 ps Last frame written was 10008, time 70056.00 ps Why this occurs ? Because you're telling trjcat that both trajectories start at the same time, so they're going to overwrite one another. If they are indeed two separate segments of a continuous trajectory, they need different start times, one zero and one non-zero. By the way if I'm using -cat option resulted file consist of both trajectories ( in the separate enties). That's what -cat is designed to do. I doubt you want that in this case. The times will still be wrong. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * 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 * Only plain text messages are allowed! * 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] About Surface tension in lipid simulation.....
Hi Gromacs Friends, I completed the Justin Protein KALP - lipid tutorial ... I want to simulate the DPPC lipid bilayer membrane under Stress condition ( Lateral tension = 20 mNm/m).. For stress condition I made the following npt.mdp ; Temperature coupling is on tcoupl = Berendsen; More accurate thermostat tc-grps = Protein DPPCSOL_CL; three coupling groups more accurate tau_t= 0.10.10.1; time constant, in ps ref_t = 323 323323; reference temperature,one for each group, ; Pressure coupling is on pcoupl = Berendsen; Pressure coupling on in NPT pcoupltype = ??; uniform scaling of x-y box vectors, independent z tau_p = 0.5; time constant, in ps ref_p = -30.01.0; reference pressure, x-y, z (in bar) compressibility = 5.0e-55.0e-5; isothermal compressibility, bar^-1 What pcoupl type Should be used Semisotropic or Surface tension.. and why??? Thank you in advance... With Best Wishes and regards , Rama. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] dihedral correlation function g_angle and g_chi
Dear All, A quick question, here g_angle with the -oc word can compute the dihedral correlation function C(t) as well as g_chi with -corr argument . Do these tools use the same approach discussed in the paper of van der Spoel and Berendsen 1997 BJ 72 2032.to compute C(t) ? Thank you for the precision. Stephane -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] 1replica/1cpu problem
Dear gromacs users, I am trying to run a replica exchange simulation using the files you find in http://dl.dropbox.com /u/40545409/gmx_mailinglist/inputs.tgz The 4 replicas have been generated, as following: grompp -p rest2.top -c 03md.gro -n index.ndx -o rest2_0 -f rest2_0.mdp grompp -p rest2.top -c 03md.gro -n index.ndx -o rest2_1 -f rest2_1.mdp grompp -p rest2.top -c 03md.gro -n index.ndx -o rest2_2 -f rest2_2.mdp grompp -p rest2.top -c 03md.gro -n index.ndx -o rest2_3 -f rest2_3.mdp The simulation was started with command, using gromacs 4.5.5 with the latest bug fix: mpirun -np 4 mdrun_mpi -s rest2_.tpr -multi 4 -replex 1000 out1 giving the following error: [etna:10799] *** An error occurred in MPI_comm_size [etna:10799] *** on communicator MPI_COMM_WORLD [etna:10799] *** MPI_ERR_COMM: invalid communicator [etna:10799] *** MPI_ERRORS_ARE_FATAL (your MPI job will now abort) -- mpirun has exited due to process rank 0 with PID 10796 on node etna exiting without calling finalize. This may have caused other processes in the application to be terminated by signals sent by mpirun (as reported here). -- [etna:10795] 3 more processes have sent help message help-mpi-errors.txt / mpi_errors_are_fatal [etna:10795] Set MCA parameter orte_base_help_aggregate to 0 to see all help / error messages The nice thing is that the same error doesn't appear either if I use the 4.5.5 without applying tha patches!!! mpirun -np 4 mdrun_mpi -s rest2_.tpr -multi 4 -replex 1000 out2 or the bug fixed with multiple processors per replica: mpirun -np 8 mdrun_mpi -s rest2_.tpr -multi 4 -replex 1000 out3 Since I have to use more then 4 replicas, I need to run 1cpu/replica. Has someone any idea of the probem? Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] patching residues
Hello gromacs users, I am trying to use pdb2gmx to bring my crystal structure into gromacs environment. The protein in the crystal has glycosidic linkages. In charmm, I could attach these carbohydrate structures using PATCH command. What is the equivalent of doing this in gromacs? My initial search of the gromacs manual and forums suggest I build a new residue that already incorporates this patch and add the new bonding type to the specbond.dat. However, I am looking to see if there is a more generic approach; it is likely that there I may need to attach different types of linkages, in which case, generating a new residue every time becomes tedious. Thanks, Kaushik -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] patching residues
On 7/18/12 2:41 PM, kaushik lakkaraju wrote: Hello gromacs users, I am trying to use pdb2gmx to bring my crystal structure into gromacs environment. The protein in the crystal has glycosidic linkages. In charmm, I could attach these carbohydrate structures using PATCH command. What is the equivalent of doing this in gromacs? My initial search of the gromacs manual and forums suggest I build a new residue that already incorporates this patch and add the new bonding type to the specbond.dat. However, I am looking to see if there is a more generic approach; it is likely that there I may need to attach different types of linkages, in which case, generating a new residue every time becomes tedious. This is the correct approach, and to my knowledge, the most efficient way that Gromacs allows to create non-linear linkages. pdb2gmx can only create linear linkages between residues in a sequence unless specbond.dat is used to create branch points in a chain. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * 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] hydrogen bond between polymer and water
Dear Gromacs users, I am calculating hydrogen bonds between polymer and water using Gromacs 4.5.4 and opls-AA force field. Our goal is to extract coordinates of atoms which form hydrogen bond at each frame. 1. The way I do it now is iterating following commands at every frame using a script: g_hbond -f fn -s fn -b frame# -e frame# -g frame# trjconv -f fn -s fn -b frame# -e frame# -o frame#.pdb It works but would take 5ns and generate 0.6GB data per 100 frame for my system. Since Gromacs can calculate the hbond life time so that I wonder is there anywhere I can find hbond index for each frame? 2. Another thing weird in my simulation is : based on the hbond log file, all the hydrogen that can form hbond is HW1, which is the first hydrogen in water residue. a glimpse of my log file: # Donor Hydrogen Acceptor SOL750OW SOL750HW1 BAE380O1 SOL787OW SOL787HW1 MMA491O1 SOL824OW SOL824HW1 MMA423O1 Would you have any idea about this? Thanks in advance! -Zifeng -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] hydrogen bond between polymer and water
On 7/18/12 4:57 PM, zifeng li wrote: Dear Gromacs users, I am calculating hydrogen bonds between polymer and water using Gromacs 4.5.4 and opls-AA force field. Our goal is to extract coordinates of atoms which form hydrogen bond at each frame. 1. The way I do it now is iterating following commands at every frame using a script: g_hbond -f fn -s fn -b frame# -e frame# -g frame# trjconv -f fn -s fn -b frame# -e frame# -o frame#.pdb It works but would take 5ns and generate 0.6GB data per 100 frame for my system. Since Gromacs can calculate the hbond life time so that I wonder is there anywhere I can find hbond index for each frame? One run through g_hbond with -hbm and -hbn will map out all hydrogen bonds and when they exist. No need to analyze frames separately. 2. Another thing weird in my simulation is : based on the hbond log file, all the hydrogen that can form hbond is HW1, which is the first hydrogen in water residue. a glimpse of my log file: # Donor Hydrogen Acceptor SOL750OW SOL750HW1 BAE380O1 SOL787OW SOL787HW1 MMA491O1 SOL824OW SOL824HW1 MMA423O1 Would you have any idea about this? The default behavior of g_hbond is to merge equivalent hydrogens (-merge flag) so HW1 and HW2 are considered the same and likely are just labeled as HW1. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * 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] Gromacs 54a7 force field
Hi all... I heard that gromos 54a7 ff is much better for simulations than 53a6. i have a membrane protein system. To simulate it, should I include the berger lipid parameters manually as shown in justin Lemkul's membrane protein tutorial? Thanks -- View this message in context: http://gromacs.5086.n6.nabble.com/Gromacs-54a7-force-field-tp4999538.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Gromacs 54a7 force field
On 7/18/12 5:37 PM, Rajat Desikan wrote: Hi all... I heard that gromos 54a7 ff is much better for simulations than 53a6. i have a membrane protein system. To simulate it, should I include the berger lipid parameters manually as shown in justin Lemkul's membrane protein tutorial? The Berger parameters should (in theory) be compatible, but 54A7 also introduced changes to the Gromos96 lipid parameters. Whatever force field you determine to be the best is included in the same manner as the tutorial suggests. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * 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: Gromacs 54a7 force field
54A7 also introduced changes to the Gromos96 lipid parameters How will this change my inclusion of the berger lipid parameters? Any thing that I should pay special attention to? Are there other lipid parameters more compatible? I heard from a faculty member at our Institute that the 53a6 is a bad ff for a protein with a lot of alpha helices for longer simulations. She apparently saw the helices unravel when they were supposed to be stable. -- View this message in context: http://gromacs.5086.n6.nabble.com/Gromacs-54a7-force-field-tp4999538p4999540.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Gromacs 54a7 force field
On 7/18/12 5:51 PM, Rajat Desikan wrote: 54A7 also introduced changes to the Gromos96 lipid parameters How will this change my inclusion of the berger lipid parameters? Any thing that I should pay special attention to? Are there other lipid parameters more compatible? There are better force fields for lipids, but they require the use of CHARMM. There may be other suitable united atom force fields. My comment was intentionally generic; I don't know how well 54A7 pairs with the Berger parameters. In theory, it should be fine, but since Gromos96 parameters for lipids have been tweaked, maybe the balance of forces in the parameters for proteins and lipids will be affected. There was a new lipid atom type introduced to make Gromos96 lipids better. They're still not as good as CHARMM, though. I heard from a faculty member at our Institute that the 53a6 is a bad ff for a protein with a lot of alpha helices for longer simulations. She apparently saw the helices unravel when they were supposed to be stable. This is a hot topic. Conventional wisdom does demonstrate that 53A6 destabilizes helices, but others will contend that 53A6 is perfectly suitable for reproducing many experimental observables, including NMR signals. I tend to think that there is some bias, but all force fields have shortcomings. 54A7 is certainly better in terms of helical stabilization, from what I can see. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * 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: Gromacs 54a7 force field
Thanks for the quick and detailed replies Justin :) This helped clear some doubts I had. I thought all Charmm ff were compatible in Gromacs? Which Charmm ff were you referring to? -- View this message in context: http://gromacs.5086.n6.nabble.com/Gromacs-54a7-force-field-tp4999538p4999542.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Gromacs 54a7 force field
On 7/18/12 6:13 PM, Rajat Desikan wrote: Thanks for the quick and detailed replies Justin :) This helped clear some doubts I had. I thought all Charmm ff were compatible in Gromacs? Which Charmm ff were you referring to? CHARMM force fields are largely just sequential additions and refinements of previous versions. The CHARMM36 parameter set uses CHARMM27 protein parameters with optimized lipid parameters, IIRC. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * 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: Gromacs 54a7 force field
So CHARMM36 would be the best ff for a long membrane protein simulation? Is it possible to integrate CHARMM36 into Gromacs? -- View this message in context: http://gromacs.5086.n6.nabble.com/Gromacs-54a7-force-field-tp4999538p4999544.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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: Gromacs 54a7 force field
I got the answer to whether we can implement CHARMM36 into gromacs...:) thanks http://www.gromacs.org/Downloads/User_contributions/Force_fields I still want your opinion on whether it is the best ff for simulating a membrane-protein system, and if any modifications to the ff are necessary? Thanks -- View this message in context: http://gromacs.5086.n6.nabble.com/Gromacs-54a7-force-field-tp4999538p4999545.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Gromacs 54a7 force field
Hi, Justin, I am interested by your comments regarding the CHARMM lipids. In particular can you elaborate as to why you think that the CHARMM lipids are better than the united-atom ones (such as Berger and several GROMOS variants). As for the original question, the modifications in going from GROMOS 53A6 to 54A7 will not influence the combination with the Berger lipid parameters, if the most common approach of using the parameters from the 'lipid.itp' file is taken. The interactions between protein and lipid will remain the same, with the van der Waals interactions between the protein and lipid treated using the GROMOS87 parameters as defined in lipid.itp. From my experiences I would strongly recommend using 54A7 over 53A6, as we have seen instability in short helices in 53A6 that is not reproduced when simulating the same systems with several other force fields. For the 'best' force field to choose when simulating a membrane-protein system, there is no definitive answer that I (or anyone else) can give you (yet). My own opinion is that currently CHARMM36 is probably too slow (given that I would strongly recommend the use of the CHARMM TIP3P water model with this force field) and that the all-atom protein force fields are probably better than the united-atom ones. This means that I would (for a PC membrane) use Berger for the lipids with OPLS-AA/L or an AMBER force field for the protein. This is just my (current) opinion though, I strongly suggest doing lots of your own reading before making your mind up. Cheers Tom On 18/07/12 22:55, Justin Lemkul wrote: On 7/18/12 5:51 PM, Rajat Desikan wrote: 54A7 also introduced changes to the Gromos96 lipid parameters How will this change my inclusion of the berger lipid parameters? Any thing that I should pay special attention to? Are there other lipid parameters more compatible? There are better force fields for lipids, but they require the use of CHARMM. There may be other suitable united atom force fields. My comment was intentionally generic; I don't know how well 54A7 pairs with the Berger parameters. In theory, it should be fine, but since Gromos96 parameters for lipids have been tweaked, maybe the balance of forces in the parameters for proteins and lipids will be affected. There was a new lipid atom type introduced to make Gromos96 lipids better. They're still not as good as CHARMM, though. I heard from a faculty member at our Institute that the 53a6 is a bad ff for a protein with a lot of alpha helices for longer simulations. She apparently saw the helices unravel when they were supposed to be stable. This is a hot topic. Conventional wisdom does demonstrate that 53A6 destabilizes helices, but others will contend that 53A6 is perfectly suitable for reproducing many experimental observables, including NMR signals. I tend to think that there is some bias, but all force fields have shortcomings. 54A7 is certainly better in terms of helical stabilization, from what I can see. -Justin -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Gromacs 54a7 force field
On 7/18/12 6:57 PM, Thomas Piggot wrote: Hi, Justin, I am interested by your comments regarding the CHARMM lipids. In particular can you elaborate as to why you think that the CHARMM lipids are better than the united-atom ones (such as Berger and several GROMOS variants). I think there's nothing wrong with Berger lipids, and I myself use them routinely. They do a decent job of reproducing lipid behavior, no question. My own use is motivated by historical reasons primarily since I began work with them many years ago (also around the time that 53A6 was all shiny and new) and I'm trying to keep consistent. It seems to me that the CHARMM36 parameters are very thoroughly validated and are very modern. The Berger lipids were developed a long time ago using very short (by modern comparisons) simulations and old parameter sets that have since been improved upon. There are numerous reasonable lipid models out there, to be sure. As for the original question, the modifications in going from GROMOS 53A6 to 54A7 will not influence the combination with the Berger lipid parameters, if the most common approach of using the parameters from the 'lipid.itp' file is taken. The interactions between protein and lipid will remain the same, with the van der Waals interactions between the protein and lipid treated using the GROMOS87 parameters as defined in lipid.itp. From my experiences I would strongly recommend using 54A7 over 53A6, as we have seen instability in short helices in 53A6 that is not reproduced when simulating the same systems with several other force fields. I agree with this, I'm just a stickler for validation. A test system using this force field combination should certainly replicate some known behavior. It's generally accepted that any Gromos derivative is compatible with the Berger parameters, but I've never seen anyone demonstrate it systematically aside from their own usage for particular cases. For the 'best' force field to choose when simulating a membrane-protein system, there is no definitive answer that I (or anyone else) can give you (yet). My own opinion is that currently CHARMM36 is probably too slow (given that I would strongly recommend the use of the CHARMM TIP3P water model with this force field) and that the all-atom protein force fields are probably better than the united-atom ones. This means that I would (for a PC membrane) use Berger for the lipids with OPLS-AA/L or an AMBER force field for the protein. This is just my (current) opinion though, I strongly suggest doing lots of your own reading before making your mind up. Indeed. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Gromacs 54a7 force field
Hi, Yes, I agree with you regarding the combination of Berger and GROMOS force field and requiring validation. I just wanted to point out the interactions between the protein and lipid are treated in the same way, irrespective of the different GROMOS protein force field used (when using the parameters from lipid.itp). Further on the topic of validation, the only work I know of that has studied in detail the Berger/GROMOS combination (doi:10.1088/0953-8984/18/28/S07) says that when using the standard method as employed by the parameters in lipid.itp: the strength of interactions between hydrocarbon lipid tails and proteins is significantly overestimated, causing a decrease in the area per lipid and an increase in lipid ordering So the standard approach is probably not the most appropriate way to combine the Berger lipids and the GROMOS protein force field. Rather using combination rules (as for example done in the Berger/OPLS combination) is probably better. Cheers Tom On 19/07/12 00:15, Justin Lemkul wrote: On 7/18/12 6:57 PM, Thomas Piggot wrote: Hi, Justin, I am interested by your comments regarding the CHARMM lipids. In particular can you elaborate as to why you think that the CHARMM lipids are better than the united-atom ones (such as Berger and several GROMOS variants). I think there's nothing wrong with Berger lipids, and I myself use them routinely. They do a decent job of reproducing lipid behavior, no question. My own use is motivated by historical reasons primarily since I began work with them many years ago (also around the time that 53A6 was all shiny and new) and I'm trying to keep consistent. It seems to me that the CHARMM36 parameters are very thoroughly validated and are very modern. The Berger lipids were developed a long time ago using very short (by modern comparisons) simulations and old parameter sets that have since been improved upon. There are numerous reasonable lipid models out there, to be sure. As for the original question, the modifications in going from GROMOS 53A6 to 54A7 will not influence the combination with the Berger lipid parameters, if the most common approach of using the parameters from the 'lipid.itp' file is taken. The interactions between protein and lipid will remain the same, with the van der Waals interactions between the protein and lipid treated using the GROMOS87 parameters as defined in lipid.itp. From my experiences I would strongly recommend using 54A7 over 53A6, as we have seen instability in short helices in 53A6 that is not reproduced when simulating the same systems with several other force fields. I agree with this, I'm just a stickler for validation. A test system using this force field combination should certainly replicate some known behavior. It's generally accepted that any Gromos derivative is compatible with the Berger parameters, but I've never seen anyone demonstrate it systematically aside from their own usage for particular cases. For the 'best' force field to choose when simulating a membrane-protein system, there is no definitive answer that I (or anyone else) can give you (yet). My own opinion is that currently CHARMM36 is probably too slow (given that I would strongly recommend the use of the CHARMM TIP3P water model with this force field) and that the all-atom protein force fields are probably better than the united-atom ones. This means that I would (for a PC membrane) use Berger for the lipids with OPLS-AA/L or an AMBER force field for the protein. This is just my (current) opinion though, I strongly suggest doing lots of your own reading before making your mind up. Indeed. -Justin -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] 1replica/1cpu problem
On 19/07/2012 12:32 AM, francesco oteri wrote: Dear gromacs users, I am trying to run a replica exchange simulation using the files you find in http://dl.dropbox.com /u/40545409/gmx_mailinglist/inputs.tgz The 4 replicas have been generated, as following: grompp -p rest2.top -c 03md.gro -n index.ndx -o rest2_0 -f rest2_0.mdp grompp -p rest2.top -c 03md.gro -n index.ndx -o rest2_1 -f rest2_1.mdp grompp -p rest2.top -c 03md.gro -n index.ndx -o rest2_2 -f rest2_2.mdp grompp -p rest2.top -c 03md.gro -n index.ndx -o rest2_3 -f rest2_3.mdp The simulation was started with command, using gromacs 4.5.5 with the latest bug fix: Which bug fix? How did you apply it? Mark mpirun -np 4 mdrun_mpi -s rest2_.tpr -multi 4 -replex 1000 out1 giving the following error: [etna:10799] *** An error occurred in MPI_comm_size [etna:10799] *** on communicator MPI_COMM_WORLD [etna:10799] *** MPI_ERR_COMM: invalid communicator [etna:10799] *** MPI_ERRORS_ARE_FATAL (your MPI job will now abort) -- mpirun has exited due to process rank 0 with PID 10796 on node etna exiting without calling finalize. This may have caused other processes in the application to be terminated by signals sent by mpirun (as reported here). -- [etna:10795] 3 more processes have sent help message help-mpi-errors.txt / mpi_errors_are_fatal [etna:10795] Set MCA parameter orte_base_help_aggregate to 0 to see all help / error messages The nice thing is that the same error doesn't appear either if I use the 4.5.5 without applying tha patches!!! mpirun -np 4 mdrun_mpi -s rest2_.tpr -multi 4 -replex 1000 out2 or the bug fixed with multiple processors per replica: mpirun -np 8 mdrun_mpi -s rest2_.tpr -multi 4 -replex 1000 out3 Since I have to use more then 4 replicas, I need to run 1cpu/replica. Has someone any idea of the probem? Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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
