Re: [gmx-users] g_sas query
Hey Anirban, I would consider the ions part of the solvent. But the procedure is right. Cheers, Tsjerk On May 7, 2011 7:35 AM, Anirban Ghosh reach.anirban.gh...@gmail.com wrote: Hi ALL, I want to calculate the SASA of a protein embedded in a bilayer along with water and ions. So while using g_sas I understand that I need to supply all non-solvent atoms as calculation group and Protein as the output group. So I need to make a group with Protein+Lipid+Ions as the calculation group. Right? Thanks a lot in advance. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_sas query
Hello Tsjerk, Thanks for the reply. But if I consider the ions also in the calculation group, then it is not wrong. Right? Thanks, Anirban On Sat, May 7, 2011 at 11:59 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hey Anirban, I would consider the ions part of the solvent. But the procedure is right. Cheers, Tsjerk On May 7, 2011 7:35 AM, Anirban Ghosh reach.anirban.gh...@gmail.com wrote: Hi ALL, I want to calculate the SASA of a protein embedded in a bilayer along with water and ions. So while using g_sas I understand that I need to supply all non-solvent atoms as calculation group and Protein as the output group. So I need to make a group with Protein+Lipid+Ions as the calculation group. Right? Thanks a lot in advance. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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] g_sas query
On 7/05/2011 4:36 PM, Anirban Ghosh wrote: Hello Tsjerk, Thanks for the reply. But if I consider the ions also in the calculation group, then it is not wrong. Right? Only you know where your ions are, and whether their contribution to surface area means anything. Make the hybrid groups accordingly. Mark Thanks, Anirban On Sat, May 7, 2011 at 11:59 AM, Tsjerk Wassenaar tsje...@gmail.com mailto:tsje...@gmail.com wrote: Hey Anirban, I would consider the ions part of the solvent. But the procedure is right. Cheers, Tsjerk On May 7, 2011 7:35 AM, Anirban Ghosh reach.anirban.gh...@gmail.com mailto:reach.anirban.gh...@gmail.com wrote: Hi ALL, I want to calculate the SASA of a protein embedded in a bilayer along with water and ions. So while using g_sas I understand that I need to supply all non-solvent atoms as calculation group and Protein as the output group. So I need to make a group with Protein+Lipid+Ions as the calculation group. Right? Thanks a lot in advance. Regards, Anirban -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] liquid/liquid
Hi all I want to simulate a liquid/liquid interface. After construction one of them in one side of the box and the other in the another side, I want to all some other molecules randomly in one of them. What should I do? Would you please help me? Thanks alot Maria -- 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] Fwd: liquid/liquid
-- Forwarded message -- From: Maria Hamilton hamilton.mari...@gmail.com Date: Sat, May 7, 2011 at 12:33 PM Subject: liquid/liquid To: gmx-users@gromacs.org Hi all I want to simulate a liquid/liquid interface. After construction one of them in one side of the box and the other in the another side, I want to all some other molecules randomly in one of them. What should I do? You may gauss the third molecule should be distribute randomly in second liquid. Would you please help me? Thanks alot Maria -- 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] On posre.itp
Hi everyone! I was able to generate a pdb file in which the hydrogens for the molecule are already included (that way I avoided using the hdb file for the pdb2gmx). However, when I checked the posre.itp, the some of the restraints were applied to the hydrogens. Is this correct because I am not sure since I what I know is that the restraints should be applied to heavy atoms. Are the positional restraints needed only for the equalibration step but not for the production runs in normal MD simulations. Thanks. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_sas query
Hello Tsjerk Mark, Thanks for the reply. Actually more important than the ions is the lipid bilayer of my system. Actually my protein is a GPCR embedded in a lipid bilayer. So when I want to calculate the SASA of my protein, so should I use a group (Protein+Lipid+Ions) as the calculation group and Protein as the output group? Thanks again, Anirban On Sat, May 7, 2011 at 1:05 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 7/05/2011 4:36 PM, Anirban Ghosh wrote: Hello Tsjerk, Thanks for the reply. But if I consider the ions also in the calculation group, then it is not wrong. Right? Only you know where your ions are, and whether their contribution to surface area means anything. Make the hybrid groups accordingly. Mark Thanks, Anirban On Sat, May 7, 2011 at 11:59 AM, Tsjerk Wassenaar tsje...@gmail.comwrote: Hey Anirban, I would consider the ions part of the solvent. But the procedure is right. Cheers, Tsjerk On May 7, 2011 7:35 AM, Anirban Ghosh reach.anirban.gh...@gmail.com wrote: Hi ALL, I want to calculate the SASA of a protein embedded in a bilayer along with water and ions. So while using g_sas I understand that I need to supply all non-solvent atoms as calculation group and Protein as the output group. So I need to make a group with Protein+Lipid+Ions as the calculation group. Right? Thanks a lot in advance. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] liquid/liquid
On 7/05/2011 6:03 PM, Maria Hamilton wrote: Hi all I want to simulate a liquid/liquid interface. After construction one of them in one side of the box and the other in the another side, I want to all some other molecules randomly in one of them. What should I do? There's a tutorial about such biphasic systems, which I hope you searched for first, before emailing :-) Probably you can adapt that by doing your insertion at a suitable point. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_sas query
On 7/05/2011 7:04 PM, Anirban Ghosh wrote: Hello Tsjerk Mark, Thanks for the reply. Actually more important than the ions is the lipid bilayer of my system. Actually my protein is a GPCR embedded in a lipid bilayer. So when I want to calculate the SASA of my protein, so should I use a group (Protein+Lipid+Ions) as the calculation group and Protein as the output group? We've answered the first part of this already. You should read g_sas -h for clues about the groups. Only you know whether Protein-only output is sensible for your purpose. Mark Thanks again, Anirban On Sat, May 7, 2011 at 1:05 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 7/05/2011 4:36 PM, Anirban Ghosh wrote: Hello Tsjerk, Thanks for the reply. But if I consider the ions also in the calculation group, then it is not wrong. Right? Only you know where your ions are, and whether their contribution to surface area means anything. Make the hybrid groups accordingly. Mark Thanks, Anirban On Sat, May 7, 2011 at 11:59 AM, Tsjerk Wassenaar tsje...@gmail.com mailto:tsje...@gmail.com wrote: Hey Anirban, I would consider the ions part of the solvent. But the procedure is right. Cheers, Tsjerk On May 7, 2011 7:35 AM, Anirban Ghosh reach.anirban.gh...@gmail.com mailto:reach.anirban.gh...@gmail.com wrote: Hi ALL, I want to calculate the SASA of a protein embedded in a bilayer along with water and ions. So while using g_sas I understand that I need to supply all non-solvent atoms as calculation group and Protein as the output group. So I need to make a group with Protein+Lipid+Ions as the calculation group. Right? Thanks a lot in advance. Regards, Anirban -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] On posre.itp
On 7/05/2011 7:01 PM, Mr Bernard Ramos wrote: Hi everyone! I was able to generate a pdb file in which the hydrogens for the molecule are already included (that way I avoided using the hdb file for the pdb2gmx). However, when I checked the posre.itp, the some of the restraints were applied to the hydrogens. Is this correct because I am not sure since I what I know is that the restraints should be applied to heavy atoms. Maybe your atom names are confusing pdb2gmx. Maybe you're comparing apples and oranges with the indices in the coordinate file and the indices in the posres.itp (which are relative to the [atoms], IIRC). Are the positional restraints needed only for the equalibration step but not for the production runs in normal MD simulations. Thanks. Up to you. Do you want to sample under unphysical restraints or not? Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] On posre.itp
Thanks for the response. I will be doing a simple MD without the positional restraints. How do I go about reviewing the code for posres? What I did was to add new ff parameters for a new residue I introduced. May I please know what file in the program determines the posres so that I can revew them. Thanks. --- On Sat, 5/7/11, Mark Abraham mark.abra...@anu.edu.au wrote: From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] On posre.itp To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Saturday, May 7, 2011, 5:10 PM On 7/05/2011 7:01 PM, Mr Bernard Ramos wrote: Hi everyone! I was able to generate a pdb file in which the hydrogens for the molecule are already included (that way I avoided using the hdb file for the pdb2gmx). However, when I checked the posre.itp, the some of the restraints were applied to the hydrogens. Is this correct because I am not sure since I what I know is that the restraints should be applied to heavy atoms. Maybe your atom names are confusing pdb2gmx. Maybe you're comparing apples and oranges with the indices in the coordinate file and the indices in the posres.itp (which are relative to the [atoms], IIRC). Are the positional restraints needed only for the equalibration step but not for the production runs in normal MD simulations. Thanks. Up to you. Do you want to sample under unphysical restraints or not? Mark -Inline Attachment Follows- -- 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
Re: [gmx-users] On posre.itp
I think I've got the answer. It is on the input pdb file. The heavy atoms need to be labeled properly. thanks --- On Sat, 5/7/11, Mr Bernard Ramos bgrquan...@yahoo.com wrote: From: Mr Bernard Ramos bgrquan...@yahoo.com Subject: Re: [gmx-users] On posre.itp To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Saturday, May 7, 2011, 5:16 PM Thanks for the response. I will be doing a simple MD without the positional restraints. How do I go about reviewing the code for posres? What I did was to add new ff parameters for a new residue I introduced. May I please know what file in the program determines the posres so that I can revew them. Thanks. --- On Sat, 5/7/11, Mark Abraham mark.abra...@anu.edu.au wrote: From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] On posre.itp To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Saturday, May 7, 2011, 5:10 PM On 7/05/2011 7:01 PM, Mr Bernard Ramos wrote: Hi everyone! I was able to generate a pdb file in which the hydrogens for the molecule are already included (that way I avoided using the hdb file for the pdb2gmx). However, when I checked the posre.itp, the some of the restraints were applied to the hydrogens. Is this correct because I am not sure since I what I know is that the restraints should be applied to heavy atoms. Maybe your atom names are confusing pdb2gmx. Maybe you're comparing apples and oranges with the indices in the coordinate file and the indices in the posres.itp (which are relative to the [atoms], IIRC). Are the positional restraints needed only for the equalibration step but not for the production runs in normal MD simulations. Thanks. Up to you. Do you want to sample under unphysical restraints or not? Mark -Inline Attachment Follows- -- 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 -Inline Attachment Follows- -- 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
Re: [gmx-users] On posre.itp
On 7/05/2011 7:16 PM, Mr Bernard Ramos wrote: Thanks for the response. I will be doing a simple MD without the positional restraints. How do I go about reviewing the code for posres? What I did was to add new ff parameters for a new residue I introduced. May I please know what file in the program determines the posres so that I can revew them. Thanks. Please give full descriptions the first time. I posted a noob question on the AMBER mailing list a few months back, and would never have gotten the problem solved except that I included some details that I thought were irrelevant, and someone spotted my problem. We've all got better things to do than play question-and-answer. You might have invented some atom names that pdb2gmx doesn't know how to cope with - but you haven't said whether your apparently erronously generated position restraints are specific to your new residue or not. Unfortunately you haven't shared your atom names after I suggested the atom names were probably the problem, and I'm not going to make guesses. There's various databases in $GMXLIB/share/top for various force fields, but I don't know your GROMACS version either... I don't think looking at the code will lead to a solution. Mark --- On *Sat, 5/7/11, Mark Abraham /mark.abra...@anu.edu.au/* wrote: From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] On posre.itp To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Saturday, May 7, 2011, 5:10 PM On 7/05/2011 7:01 PM, Mr Bernard Ramos wrote: Hi everyone! I was able to generate a pdb file in which the hydrogens for the molecule are already included (that way I avoided using the hdb file for the pdb2gmx). However, when I checked the posre.itp, the some of the restraints were applied to the hydrogens. Is this correct because I am not sure since I what I know is that the restraints should be applied to heavy atoms. Maybe your atom names are confusing pdb2gmx. Maybe you're comparing apples and oranges with the indices in the coordinate file and the indices in the posres.itp (which are relative to the [atoms], IIRC). Are the positional restraints needed only for the equalibration step but not for the production runs in normal MD simulations. Thanks. Up to you. Do you want to sample under unphysical restraints or not? Mark -Inline Attachment Follows- -- gmx-users mailing list gmx-users@gromacs.org http://us.mc1615.mail.yahoo.com/mc/compose?to=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 http://us.mc1615.mail.yahoo.com/mc/compose?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] How to recenter solvent around solute
Hello, I have performed simulations of protein+ligands (solute) in truncated octahedral unit cell of waters (solvent). I would like to retain the shape of unit cell and have the solute centered in such a way as to be completely surrounded by solvent. At this point, I cannot achieve this although I have exhausted my knowledge about using the trjconv options. My question is: 1. How can one recenter solvent around solute and at the same time keep the original unit shape? I used the following command to get this picture: trjconv -f run.xtc -s run.tpr -n index-all.ndx -o traj/run-test.xtc -pbc mol -center -ur compact where for centering the solute was used and the whole system was saved to the output trajectory. Thanks, Dimitar -- 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] How to recenter solvent around solute
Dimitar Pachov wrote: Hello, I have performed simulations of protein+ligands (solute) in truncated octahedral unit cell of waters (solvent). I would like to retain the shape of unit cell and have the solute centered in such a way as to be completely surrounded by solvent. At this point, I cannot achieve this although I have exhausted my knowledge about using the trjconv options. My question is: 1. How can one recenter solvent around solute and at the same time keep the original unit shape? I used the following command to get this picture: trjconv -f run.xtc -s run.tpr -n index-all.ndx -o traj/run-test.xtc -pbc mol -center -ur compact Use -ur tric instead of -ur compact. -Justin where for centering the solute was used and the whole system was saved to the output trajectory. Thanks, Dimitar -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] How to recenter solvent around solute
On Sat, May 7, 2011 at 11:02 AM, Justin A. Lemkul jalem...@vt.edu wrote: Dimitar Pachov wrote: Hello, I have performed simulations of protein+ligands (solute) in truncated octahedral unit cell of waters (solvent). I would like to retain the shape of unit cell and have the solute centered in such a way as to be completely surrounded by solvent. At this point, I cannot achieve this although I have exhausted my knowledge about using the trjconv options. My question is: 1. How can one recenter solvent around solute and at the same time keep the original unit shape? I used the following command to get this picture: trjconv -f run.xtc -s run.tpr -n index-all.ndx -o traj/run-test.xtc -pbc mol -center -ur compact Use -ur tric instead of -ur compact. This does not work. Neither is the solute always surrounded by solvent for every frame (it goes out of the box) nor is the original unit cell (truncated octahedron) preserved. I don't understand how one can achieve this, and if there is a way to do it, why it has not been clearly explained elsewhere. Thanks, Dimitar -Justin where for centering the solute was used and the whole system was saved to the output trajectory. Thanks, Dimitar -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] How to recenter solvent around solute
Dimitar Pachov wrote: On Sat, May 7, 2011 at 11:02 AM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Dimitar Pachov wrote: Hello, I have performed simulations of protein+ligands (solute) in truncated octahedral unit cell of waters (solvent). I would like to retain the shape of unit cell and have the solute centered in such a way as to be completely surrounded by solvent. At this point, I cannot achieve this although I have exhausted my knowledge about using the trjconv options. My question is: 1. How can one recenter solvent around solute and at the same time keep the original unit shape? I used the following command to get this picture: trjconv -f run.xtc -s run.tpr -n index-all.ndx -o traj/run-test.xtc -pbc mol -center -ur compact Use -ur tric instead of -ur compact. This does not work. Neither is the solute always surrounded by solvent for every frame (it goes out of the box) nor is the original unit cell (truncated octahedron) preserved. Please clarify - do you wish to maintain the original triclinic representation (as -ur tric does) or do you wish to see the octahedral representation (as -pbc mol -ur compact gives)? My answer was based on your request to keep the original unit shape. I don't understand how one can achieve this, and if there is a way to do it, why it has not been clearly explained elsewhere. For complicated systems (or sometimes even for simple ones), it is quite common that multiple iterations of trjconv are necessary. A suggested workflow is indeed documented: http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow The documentation must remain somewhat generic, as there are a number of specialty systems that can be considered. -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
