Re: [gmx-users] mismatch in coordinate and topology
Hi Justin, No. I have not added any ions. Samrat From: Justin A. Lemkul To: Discussion list for GROMACS users Sent: Friday, October 21, 2011 11:39 AM Subject: Re: [gmx-users] mismatch in coordinate and topology Samrat Pal wrote: > Hi Justin, > (1) None of the ligands have 31 atoms - FAD has 86 atoms and MHF has >54 atoms. The error msg. does not show any specific mismatching. > (2) I forgot to mention that I have increased the number of the atoms on the >top (2nd line) of the gro file after adding the 2 ligands. > Did you add any ions after solvation? And if so, did you update your topology? If SOL is the last entry, then likely not. -Justin > Samrat > *From:* Justin A. Lemkul > *To:* Samrat Pal ; Discussion list for GROMACS users > > *Sent:* Friday, October 21, 2011 8:49 AM > *Subject:* Re: [gmx-users] mismatch in coordinate and topology > > > > Samrat Pal wrote: > > Hi All, > > I am trying to minimize the chryptochrome structure that has one >FAD and one MHF ligand bound to it. > > Following are the steps that I performed > > (1) Created the protein coordinate(gro) file using pdb2gmx command and >choosing GROMOS43a1 force-field > > (2) Created the FAD and MHF topology and coordinate files using PRODRG >where I have chosen > > a) no chirality, b) full charge and (c) no minimization. /I have not seen >any option for choosing force-field in the server/. (3) I have taken the >corresponding coordinate and topology files from that server, appended the >coordinates of both the ligands in the gro file of the protein (before the box >vector i.e. the last line), and also included the ligand topology files in the >topol.top file after "posre.itp" and before "spc.itp"accordingly. > > Regarding (2) and (3) - the output of the PRODRG server will likely give poor > results. See the paper linked from > http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips. > > > (4) I have also added two lines in the [molecules] section like, > > FAD 1 > > MHF 1 > > (5) Then I have created a cubic box where I have taken the coordinate and >solvated the protein+ligands coordinate with spc water model using genbox. > > > A dodecahedral box is likely going to be more efficient, but this is not > relevant to the problem at hand. > > > (6) Then I tried to create the em.tpr file from em.mdp file using grompp >command. > > I got the following error message --- number of atoms in the coordinate >file does not match with topology file where topology file has 31 missing >atoms according to the numbers shown in the error message. > > > OK, so do any of your molecules consist of 31 atoms? Do you get any notes > about non-matching names? > > > I have checked the topology file after solvation and it is updated having >the last line of the file with SOL 34741. > > I have been using gromacs for few months and I have successfully >simulated systems with ligands before. Could anybody please tell me where I am >doing wrong? > Did you properly increment the number of atoms in the coordinate file after > adding your ligands? > > -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 > > > > -- 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@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 Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/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
Re: [gmx-users] mismatch in coordinate and topology
Hi Justin, (1) None of the ligands have 31 atoms - FAD has 86 atoms and MHF has 54 atoms. The error msg. does not show any specific mismatching. (2) I forgot to mention that I have increased the number of the atoms on the top (2nd line) of the gro file after adding the 2 ligands. Samrat From: Justin A. Lemkul To: Samrat Pal ; Discussion list for GROMACS users Sent: Friday, October 21, 2011 8:49 AM Subject: Re: [gmx-users] mismatch in coordinate and topology Samrat Pal wrote: > Hi All, > I am trying to minimize the chryptochrome structure that has one FAD >and one MHF ligand bound to it. > Following are the steps that I performed > (1) Created the protein coordinate(gro) file using pdb2gmx command and >choosing GROMOS43a1 force-field > (2) Created the FAD and MHF topology and coordinate files using PRODRG where >I have chosen > a) no chirality, b) full charge and (c) no minimization. /I have not seen any > option for choosing force-field in the server/. (3) I have taken the > corresponding coordinate and topology files from that server, appended the > coordinates of both the ligands in the gro file of the protein (before the > box vector i.e. the last line), and also included the ligand topology files > in the topol.top file after "posre.itp" and before "spc.itp"accordingly. Regarding (2) and (3) - the output of the PRODRG server will likely give poor results. See the paper linked from http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips. > (4) I have also added two lines in the [molecules] section like, > FAD 1 > MHF 1 > (5) Then I have created a cubic box where I have taken the coordinate and >solvated the protein+ligands coordinate with spc water model using genbox. > A dodecahedral box is likely going to be more efficient, but this is not relevant to the problem at hand. > (6) Then I tried to create the em.tpr file from em.mdp file using grompp > command. > I got the following error message --- number of atoms in the coordinate file >does not match with topology file where topology file has 31 missing atoms >according to the numbers shown in the error message. > OK, so do any of your molecules consist of 31 atoms? Do you get any notes about non-matching names? > I have checked the topology file after solvation and it is updated having the > last line of the file with SOL 34741. > I have been using gromacs for few months and I have successfully simulated >systems with ligands before. Could anybody please tell me where I am doing >wrong? Did you properly increment the number of atoms in the coordinate file after adding your ligands? -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
[gmx-users] mismatch in coordinate and topology
Hi All, I am trying to minimize the chryptochrome structure that has one FAD and one MHF ligand bound to it. Following are the steps that I performed (1) Created the protein coordinate(gro) file using pdb2gmx command and choosing GROMOS43a1 force-field (2) Created the FAD and MHF topology and coordinate files using PRODRG where I have chosen a) no chirality, b) full charge and (c) no minimization. I have not seen any option for choosing force-field in the server. (3) I have taken the corresponding coordinate and topology files from that server, appended the coordinates of both the ligands in the gro file of the protein (before the box vector i.e. the last line), and also included the ligand topology files in the topol.top file after "posre.itp" and before "spc.itp"accordingly. (4) I have also added two lines in the [molecules] section like, FAD 1 MHF 1 (5) Then I have created a cubic box where I have taken the coordinate and solvated the protein+ligands coordinate with spc water model using genbox. (6) Then I tried to create the em.tpr file from em.mdp file using grompp command. I got the following error message --- number of atoms in the coordinate file does not match with topology file where topology file has 31 missing atoms according to the numbers shown in the error message. I have checked the topology file after solvation and it is updated having the last line of the file with SOL 34741. I have been using gromacs for few months and I have successfully simulated systems with ligands before. Could anybody please tell me where I am doing wrong? thanks in advance Samrat -- 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] thermodynamic integration with implicit solvent
Hi All, Is it possible to use thermodynamic integration method with implicit solvent model in gromacs 4.5.4? Thanks Samrat-- 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] compressing two selections or just the reverse of pulling simulation
Oh! Thanks a lot. Samrat From: Justin A. Lemkul To: Discussion list for GROMACS users Sent: Mon, November 15, 2010 6:16:51 PM Subject: Re: [gmx-users] compressing two selections or just the reverse of pulling simulation Samrat Pal wrote: > Hi All, > In general what we do in pulling simulations that we pull one >selection keeping the other fixed. In that case the distance between the two >selections increases with time. Now, I want to push the selections i.e. one >selection will be kept fixed and the other will be pushed towards the fixed >one >so that the distance between the two selection will decrease. Is it possible >to >do that in GROMACS? What should I modify in the mdp file? I am attaching a mdp >file that I have used for pulling simulations (only the pull part). > ; pull code > pull = umbrella > pull_geometry = distance > pull_dim = N N Y > pull_start = yes > pull_ngroups = 1 > pull_group0 = freeze > pull_group1 = pull > pull_rate1 = 0.01 > pull_k1 = 1000 > I have used pull_dim N N Y as I am interested to pull only in the z >direction. >Should I just use N N -Y to do the compressing simulations? > You can't specify "negative yes" for a pulling direction. Instead, just set the pull rate to, i.e., -0.01 to pull in the opposite direction. -Justin > Please suggest. > Thanks in advance. > Samrat > -- 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@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
[gmx-users] compressing two selections or just the reverse of pulling simulation
Hi All, In general what we do in pulling simulations that we pull one selection keeping the other fixed. In that case the distance between the two selections increases with time. Now, I want to push the selections i.e. one selection will be kept fixed and the other will be pushed towards the fixed one so that the distance between the two selection will decrease. Is it possible to do that in GROMACS? What should I modify in the mdp file? I am attaching a mdp file that I have used for pulling simulations (only the pull part). ; pull code pull = umbrella pull_geometry = distance pull_dim = N N Y pull_start = yes pull_ngroups = 1 pull_group0 = freeze pull_group1 = pull pull_rate1 = 0.01 pull_k1 = 1000 I have used pull_dim N N Y as I am interested to pull only in the z direction. Should I just use N N -Y to do the compressing simulations? Please suggest. Thanks in advance. Samrat -- 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] negative values of force
Hi Justin, I the pullf.xvg file also, some values are negative. I am giving below the pull code - pull= umbrella pull_geometry = distance pull_dim= Y Y Y pull_start = yes pull_ngroups= 1 pull_group0 = freeze pull_group1 = pull pull_rate1 = 0.01 pull_k1 = 1000 I have given pull_dim Y Y Y as I am not pulling in a particular direction. Is it right? From: Samrat Pal To: jalem...@vt.edu; Discussion list for GROMACS users Sent: Sat, August 14, 2010 11:00:37 AM Subject: Re: [gmx-users] negative values of force Thanks a lot. Best Samrat From: Justin A. Lemkul To: Gromacs Users' List Sent: Sat, August 14, 2010 10:50:05 AM Subject: Re: [gmx-users] negative values of force Samrat Pal wrote: > (1) I have got the pull.xvg file from the simulation. But there the data >resolution is very high e.g after every 2 ps. But I don' need that. So, I >tried >to create a new .xvg file with lower resolution of data e.g. after every 50 >ps. >So, I used the g_traj command. > Then you should have chosen a better value of pull_nstfout. Otherwise, you can write a simple script to parse out data at more useful intervals. > (2) So, there is no error in getting the negative value of force, right? > No. Force is a vector quantity. Depending on the direction of motion of a particular atom, the force may be moving it in a positive or negative direction. This is very fundamental physics. > (3) I have also created a dist.xvg file by applying g_dist command. Can I use >force.xvg (created by g_traj) and dist.xvg (created by g_dist) files to get >force vs. extension profile? Again, the actual pull output (pullx.xvg) should be a suitable match for your pullf.xvg data. -Justin > Best > Samrat > > *From:* Justin A. Lemkul > *To:* Discussion list for GROMACS users > *Sent:* Sat, August 14, 2010 10:34:25 AM > *Subject:* Re: [gmx-users] negative values of force > > > > Samrat Pal wrote: > > Dear All, > > I have pulled a protein by keeping n-terminus fixed and > pulling >the c-terminus. I tried to extract the force.xvg profile from the .trr file by >the following command - > > > > If you've applied the pull code, is there some reason that the pullf.xvg file >does not contain the information you're looking for? > > > g_traj -f traj.trr -s pull.tpr -of force.xvg > > > > But in the force.xvg profile I am getting both positive and negative > values >of force. What does it mean? Please suggest. > > Simple Newtonian physics. g_traj is extracting instantaneous forces on the >constituent atoms, as stored in the .trr file, so all effects are considered - >pull force, intermolecular collisions, etc. > > -Justin > > > Samrat > > -- > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu<http://vt.edu> | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- gmx-users mailing listgmx-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/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/mailing_lists/users.php > -- 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] negative values of force
Thanks a lot. Best Samrat From: Justin A. Lemkul To: Gromacs Users' List Sent: Sat, August 14, 2010 10:50:05 AM Subject: Re: [gmx-users] negative values of force Samrat Pal wrote: > (1) I have got the pull.xvg file from the simulation. But there the data >resolution is very high e.g after every 2 ps. But I don' need that. So, I >tried >to create a new .xvg file with lower resolution of data e.g. after every 50 >ps. >So, I used the g_traj command. > Then you should have chosen a better value of pull_nstfout. Otherwise, you can write a simple script to parse out data at more useful intervals. > (2) So, there is no error in getting the negative value of force, right? > No. Force is a vector quantity. Depending on the direction of motion of a particular atom, the force may be moving it in a positive or negative direction. This is very fundamental physics. > (3) I have also created a dist.xvg file by applying g_dist command. Can I use >force.xvg (created by g_traj) and dist.xvg (created by g_dist) files to get >force vs. extension profile? Again, the actual pull output (pullx.xvg) should be a suitable match for your pullf.xvg data. -Justin > Best > Samrat > > *From:* Justin A. Lemkul > *To:* Discussion list for GROMACS users > *Sent:* Sat, August 14, 2010 10:34:25 AM > *Subject:* Re: [gmx-users] negative values of force > > > > Samrat Pal wrote: > > Dear All, > > I have pulled a protein by keeping n-terminus fixed and > pulling >the c-terminus. I tried to extract the force.xvg profile from the .trr file by >the following command - > > > > If you've applied the pull code, is there some reason that the pullf.xvg file >does not contain the information you're looking for? > > > g_traj -f traj.trr -s pull.tpr -of force.xvg > > > > But in the force.xvg profile I am getting both positive and negative > values >of force. What does it mean? Please suggest. > > Simple Newtonian physics. g_traj is extracting instantaneous forces on the >constituent atoms, as stored in the .trr file, so all effects are considered - >pull force, intermolecular collisions, etc. > > -Justin > > > Samrat > > -- > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu<http://vt.edu> | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- gmx-users mailing listgmx-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/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/mailing_lists/users.php > -- 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] negative values of force
(1) I have got the pull.xvg file from the simulation. But there the data resolution is very high e.g after every 2 ps. But I don' need that. So, I tried to create a new .xvg file with lower resolution of data e.g. after every 50 ps. So, I used the g_traj command. (2) So, there is no error in getting the negative value of force, right? (3) I have also created a dist.xvg file by applying g_dist command. Can I use force.xvg (created by g_traj) and dist.xvg (created by g_dist) files to get force vs. extension profile? Best Samrat From: Justin A. Lemkul To: Discussion list for GROMACS users Sent: Sat, August 14, 2010 10:34:25 AM Subject: Re: [gmx-users] negative values of force Samrat Pal wrote: > Dear All, > I have pulled a protein by keeping n-terminus fixed and pulling >the c-terminus. I tried to extract the force.xvg profile from the .trr file by >the following command - > If you've applied the pull code, is there some reason that the pullf.xvg file does not contain the information you're looking for? > g_traj -f traj.trr -s pull.tpr -of force.xvg > > But in the force.xvg profile I am getting both positive and negative values > of >force. What does it mean? Please suggest. Simple Newtonian physics. g_traj is extracting instantaneous forces on the constituent atoms, as stored in the .trr file, so all effects are considered - pull force, intermolecular collisions, etc. -Justin > Samrat -- 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] negative values of force
Dear All, I have pulled a protein by keeping n-terminus fixed and pulling the c-terminus. I tried to extract the force.xvg profile from the .trr file by the following command - g_traj -f traj.trr -s pull.tpr -of force.xvg But in the force.xvg profile I am getting both positive and negative values of force. What does it mean? Please suggest. Samrat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] pulling simulation with implicit solvent
Hi all, Can anyone please give me a mdp file for running pulling simulations in implicit solvent using GROMACS? Thanks in advance Samrat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] abnormal stop of job
Hi Elton, But I have neither killed the job nor I pressed Ctrl-C in the foreground. The job was practically running background. Thanks Atanu From: Elton Carvalho To: Discussion list for GROMACS users Sent: Thu, August 5, 2010 1:59:39 PM Subject: Re: [gmx-users] abnormal stop of job On Thu, Aug 5, 2010 at 1:37 PM, Samrat Pal wrote: > > Received the TERM signal, stopping at the next step The TERM signal is the default signal sent by the command "kill" to stop a job. Pressing Ctrl-C while the program is running on the foreground has the same effect. -- Elton Carvalho Tel.: +55 11 3091-6985/6922 Dept Física dos Materiais e Mecânica Instituto de Física Universidade de São Paulo P.O. Box 66318 - 05314-970 São Paulo-SP, Brazil -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] abnormal stop of job
Hi all, I have been running a simulation of 200 ns length and it suddenly stoped at 67 ns showing the following line - Received the TERM signal, stopping at the next step I have checked the time steps properly and there is no error. What should I do now? Please suggest. Thanks Samrat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Jarzynski equality in pulling simulation
Hi all, Just one thing to add. Generally for PMF calculation the pulling is done in one direction (N N Y in mdp file for pulling in z direction). But, as I will be pulling a protein, I think, it will be Y Y Y i.e. in all directions. Is that OK? If that so, would I be able to calculate PMF in the conventional way? Please suggest. Thanks Samrat Pal From: Samrat Pal To: Discussion list for GROMACS users Sent: Tue, July 27, 2010 2:59:01 PM Subject: Jarzynski equality in pulling simulation Dear All, I am trying to do unfolding simulation of a protein by applying pulling code in GROMACS. Now, as the pulling speed is much more faster than the optical trap experiment or the AFM experiment, what would be more logical to get the PMF/free energy of the simulation - (1) running multiple trajectories and apply Jarzynski equality to get free energy OR (2) running a single trajectory and taking configurations at different distances and then apply umbrella sampling to compute PMF. Please advise. Thanks in advance, Samrat Pal -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Jarzynski equality in pulling simulation
Dear All, I am trying to do unfolding simulation of a protein by applying pulling code in GROMACS. Now, as the pulling speed is much more faster than the optical trap experiment or the AFM experiment, what would be more logical to get the PMF/free energy of the simulation - (1) running multiple trajectories and apply Jarzynski equality to get free energy OR (2) running a single trajectory and taking configurations at different distances and then apply umbrella sampling to compute PMF. Please advise. Thanks in advance, Samrat Pal -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] implicit water model for protein folding simulation
I am trying to do some folding simulations in GROMACS. I saw few mails in the list stating that implicit water model will be available in GROMACS 4.0 version. However, I have not found anything on the implicit model in the manual. I am currently using GROMACS 4.0.7 version. Is it possible to run simulations using implicit water model (GB or something)? If that so, then please anyone give me a model .mdp file or any input file where the option for implcit model can be given. Samrat Pal -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Need For a Script
Hi Justin, I am trying to perform umbrella sampling following your link. But when I put the command grompp -f md_umbrella.mdp -c conf0.gro -p topol.top -n index.ndx -o umbrella0.tpr I found the the following error No molecules were defined in the system Could you please suggest please? Samrat. From: Samrat Pal To: jalem...@vt.edu; Discussion list for GROMACS users Sent: Mon, July 19, 2010 10:00:27 AM Subject: Re: [gmx-users] Need For a Script Another thing is that I am not sure how to get the force-extension profile from the simulation trajectory? Thanks Samrat From: Samrat Pal To: jalem...@vt.edu; Discussion list for GROMACS users Sent: Sun, July 18, 2010 12:21:04 PM Subject: Re: [gmx-users] Need For a Script I have been doing the pull simulations with your scripts and that are running fine. Thanks a lot. Can I use implicit solvent model in pulling simulations? I have gone through the mailing list and I found that it is not recommended (I may be wrong). Please suggest. Thanks in advance Samrat Pal From: Justin A. Lemkul To: Discussion list for GROMACS users Sent: Fri, July 16, 2010 5:18:44 PM Subject: Re: [gmx-users] Need For a Script Samrat Pal wrote: > Dear All, > I am a new GROMACS user. I have been able to solvate a protein in a water >box and also to simulate it and unfold it by heating it. But I have facing >problem with the script of AFM pulling. I want to unfold a protein by pulling >the two ends of the protein. Can anyone give me a full script for that so that >I >can standardise my protocol? Suggestion is urgent. http://www.gromacs.org/Documentation/Tutorials#Umbrella_Sampling Also, as a bit of advice, don't use the word "urgent" when asking for free help. You're hoping someone else (who is busy) will find time to solve an issue for you. -Justin >Thanks in advance > Samrat Pal > -- 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Need For a Script
Another thing is that I am not sure how to get the force-extension profile from the simulation trajectory? Thanks Samrat From: Samrat Pal To: jalem...@vt.edu; Discussion list for GROMACS users Sent: Sun, July 18, 2010 12:21:04 PM Subject: Re: [gmx-users] Need For a Script I have been doing the pull simulations with your scripts and that are running fine. Thanks a lot. Can I use implicit solvent model in pulling simulations? I have gone through the mailing list and I found that it is not recommended (I may be wrong). Please suggest. Thanks in advance Samrat Pal From: Justin A. Lemkul To: Discussion list for GROMACS users Sent: Fri, July 16, 2010 5:18:44 PM Subject: Re: [gmx-users] Need For a Script Samrat Pal wrote: > Dear All, > I am a new GROMACS user. I have been able to solvate a protein in a water >box and also to simulate it and unfold it by heating it. But I have facing >problem with the script of AFM pulling. I want to unfold a protein by pulling >the two ends of the protein. Can anyone give me a full script for that so that >I >can standardise my protocol? Suggestion is urgent. http://www.gromacs.org/Documentation/Tutorials#Umbrella_Sampling Also, as a bit of advice, don't use the word "urgent" when asking for free help. You're hoping someone else (who is busy) will find time to solve an issue for you. -Justin >Thanks in advance > Samrat Pal > -- 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Need For a Script
I have been doing the pull simulations with your scripts and that are running fine. Thanks a lot. Can I use implicit solvent model in pulling simulations? I have gone through the mailing list and I found that it is not recommended (I may be wrong). Please suggest. Thanks in advance Samrat Pal From: Justin A. Lemkul To: Discussion list for GROMACS users Sent: Fri, July 16, 2010 5:18:44 PM Subject: Re: [gmx-users] Need For a Script Samrat Pal wrote: > Dear All, > I am a new GROMACS user. I have been able to solvate a protein in a water >box and also to simulate it and unfold it by heating it. But I have facing >problem with the script of AFM pulling. I want to unfold a protein by pulling >the two ends of the protein. Can anyone give me a full script for that so that >I >can standardise my protocol? Suggestion is urgent. http://www.gromacs.org/Documentation/Tutorials#Umbrella_Sampling Also, as a bit of advice, don't use the word "urgent" when asking for free help. You're hoping someone else (who is busy) will find time to solve an issue for you. -Justin >Thanks in advance > Samrat Pal > -- 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Need For a Script
Hey,.. Thank you for the script. I will keep in mind what you said next time. Samrat Pal From: Justin A. Lemkul To: Discussion list for GROMACS users Sent: Fri, July 16, 2010 5:18:44 PM Subject: Re: [gmx-users] Need For a Script Samrat Pal wrote: > Dear All, > I am a new GROMACS user. I have been able to solvate a protein in a water >box and also to simulate it and unfold it by heating it. But I have facing >problem with the script of AFM pulling. I want to unfold a protein by pulling >the two ends of the protein. Can anyone give me a full script for that so that >I >can standardise my protocol? Suggestion is urgent. http://www.gromacs.org/Documentation/Tutorials#Umbrella_Sampling Also, as a bit of advice, don't use the word "urgent" when asking for free help. You're hoping someone else (who is busy) will find time to solve an issue for you. -Justin >Thanks in advance > Samrat Pal > -- 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Need For a Script
Dear All, I am a new GROMACS user. I have been able to solvate a protein in a water box and also to simulate it and unfold it by heating it. But I have facing problem with the script of AFM pulling. I want to unfold a protein by pulling the two ends of the protein. Can anyone give me a full script for that so that I can standardise my protocol? Suggestion is urgent. Thanks in advance Samrat Pal -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
