[gmx-users] POPC number
Hi gmx-users, whats the number of POPC molecules should be there after inserting protein into popc? In my case 90 popc molecules are there around the protein from 128 molecues which I downloaded from Dr.Tielman's website. Any suggestion will be appreciated Thanks in advance. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] comprehension of comm_grps
Dear GMXer, I have a protein which is stretched in one dimension and therefore use a rectangular box (filled with water/ions). To protect the protein from self interactions over the pbc, the protein may not rotate in this rectangular box. The nearest solution would be to set: comm_mode = angular comm_grps = system But (according to previous threads in this list) this would lead to clashes at the pbc boundary. Another idea would be the following setting: comm_mode = angular comm_grps = protein But I don't this would lead to one of the following two problems: A) comm_grps = protein just change the position of the calculated center of mass from the whole system to the position of the center of mass of the protein and still rotates the WHOLE SYSTEM, which would lead to the same problem described above or B) comm_grps = protein deletes just the rotation of the PROTEIN around the center of mass of the protein, which would lead to small shear forces at the surface of the protein with the water (which might perhaps be neglected). Which problem (A or B) occurs? Are there other solutions? Best wishes, Christian. -- M. Sc. Christian Seifert Department of Biophysics University of Bochum ND 04/67 44780 Bochum Germany Tel: +49 (0)234 32 28363 Fax: +49 (0)234 32 14626 E-Mail: [EMAIL PROTECTED] Web: http://www.bph.rub.de ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] POPC number
I guess that depends on the size of your protein. You should have enough lipds such that the protein doesn't interact with its preriodic image. 90 POPC seem to be a bit to few for that. In my aquaporin simulations, I usually had something like 270 POPE molecules, but if you simulate a smaller protein, less lipids may be sufficient. You may also want to use a hexagonal box which will allow you have less lipids and water. cheers, jochen sudheer babu wrote: Hi gmx-users, whats the number of POPC molecules should be there after inserting protein into popc? In my case 90 popc molecules are there around the protein from 128 molecues which I downloaded from Dr.Tielman's website. Any suggestion will be appreciated Thanks in advance. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)551 201-2312 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] simulation using POPC lipid bilayer
Dear users, I am trying to do lipid protein simulation using POPC. while running GROMPP command I am getting error Atom LC3 not found I changed POPC to POP and again ran GROMPP ,but the error is same. what should I do . Thanx in advance -- PRASUN (ASHOKA) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Position restrain of protein and membrane
minnale wrote: Thanks Justin for your kind reply, you misunderstood my query,now I am asking you clearly that, while doing membrane protein equilibration steps on which system( either protein or membrane or both) I have keep to position restrain? is there any conventional way to keep restrain? or it can change according to ourselves. I hope you understood my problem. Can you give me suggestion You can restrain whatever you like; typically just the protein is restrained. Check the literature for common protocols. -Justin Thanks in advance. minnale wrote: Hi all, I embedded protein into popc bilayer by using genbox command, in equilibration I want keep restrain only on protein but not on popc? can I do like this or is there any manditory steps to run membrane protein equibration, if it is there, Can you tell me please. Thank you. Use define = -DPOSRES which is specified in the .top from parameterizing the protein under pdb2gmx. There's nothing special (necessarily) for doing a membrane protein system, since all the topology information for the protein generally comes before the lipid/solvent stuff, anyway. -Justin Ebay http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/[EMAIL PROTECTED]/2401775_2394076/2397136/1?PARTNER=3OAS_QUERY=null ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin Rediff Shopping http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-home.htm/[EMAIL PROTECTED]/2206641_2199021/2201651/1?PARTNER=3OAS_QUERY=null ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] simulation using POPC lipid bilayer
prasun kumar wrote: Dear users, I am trying to do lipid protein simulation using POPC. while running GROMPP command I am getting error Atom LC3 not found I changed POPC to POP and again ran GROMPP ,but the error is same. what should I do . Then you haven't properly added the parameters from lipid.itp to the *nb.itp file for the force field you're using. -Justin Thanx in advance -- PRASUN (ASHOKA) ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: Re: [gmx-users] Position restrain of protein and membrane
Thanks for reply Justin, can I do this way first I will keep PR on popc later protein, I dont want keep PR on water.Can I do like this? Thanks in advance. On Tue, 16 Sep 2008 Justin A.Lemkul wrote : minnale wrote: Thanks Justin for your kind reply, you misunderstood my query,now I am asking you clearly that, while doing membrane protein equilibration steps on which system( either protein or membrane or both) I have keep to position restrain? is there any conventional way to keep restrain? or it can change according to ourselves. I hope you understood my problem. Can you give me suggestion You can restrain whatever you like; typically just the protein is restrained. Check the literature for common protocols. -Justin Thanks in advance. minnale wrote: Hi all, I embedded protein into popc bilayer by using genbox command, in equilibration I want keep restrain only on protein but not on popc? can I do like this or is there any manditory steps to run membrane protein equibration, if it is there, Can you tell me please. Thank you. Use define = -DPOSRES which is specified in the .top from parameterizing the protein under pdb2gmx. There's nothing special (necessarily) for doing a membrane protein system, since all the topology information for the protein generally comes before the lipid/solvent stuff, anyway. -Justin Ebay http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/[EMAIL PROTECTED]/2401775_2394076/2397136/1?PARTNER=3OAS_QUERY=null ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin Rediff Shopping http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-home.htm/[EMAIL PROTECTED]/2206641_2199021/2201651/1?PARTNER=3OAS_QUERY=null ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Position restrain of protein and membrane
minnale wrote: Thanks for reply Justin, can I do this way first I will keep PR on popc later protein, I dont want keep PR on water.Can I do like this? You could, but I don't see the point. In equilibrating membrane protein systems, it is very important to optimize the lipid positions around the protein at the outset of the simulation (i.e., packing). So allowing the protein to move unrestrained while restraining the lipids makes no sense (and you will probably generate some artificial interactions). You will want to apply PR to the protein, allowing the lipids to pack around it, then remove the PR from the protein and proceed with data collection. -Justin Thanks in advance. On Tue, 16 Sep 2008 Justin A.Lemkul wrote : minnale wrote: Thanks Justin for your kind reply, you misunderstood my query,now I am asking you clearly that, while doing membrane protein equilibration steps on which system( either protein or membrane or both) I have keep to position restrain? is there any conventional way to keep restrain? or it can change according to ourselves. I hope you understood my problem. Can you give me suggestion You can restrain whatever you like; typically just the protein is restrained. Check the literature for common protocols. -Justin Thanks in advance. minnale wrote: Hi all, I embedded protein into popc bilayer by using genbox command, in equilibration I want keep restrain only on protein but not on popc? can I do like this or is there any manditory steps to run membrane protein equibration, if it is there, Can you tell me please. Thank you. Use define = -DPOSRES which is specified in the .top from parameterizing the protein under pdb2gmx. There's nothing special (necessarily) for doing a membrane protein system, since all the topology information for the protein generally comes before the lipid/solvent stuff, anyway. -Justin Ebay http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/[EMAIL PROTECTED]/2401775_2394076/2397136/1?PARTNER=3OAS_QUERY=null ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin Rediff Shopping http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-home.htm/[EMAIL PROTECTED]/2206641_2199021/2201651/1?PARTNER=3OAS_QUERY=null ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin Ebay http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/[EMAIL PROTECTED]/2401775_2394076/2397136/1?PARTNER=3OAS_QUERY=null ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the
[gmx-users] Re: gmx-users Digest, Vol 53, Issue 81
http://www.gromacs.org/mailman/listinfo/gmx-users Thanks to Jochen To increase the lipid molecule number from 128(which downloaded from Dr.Tieleman site) to more than 158, I issued this command genbox -cs 128popc.gro -o out.gro -box 9.2 9.2 6.3 but in the output file it showed unequal amount water molecules on both leaflets, I have tried in changing the box values in many ways but I couldnt able to get. Can any tell me how can I solve this problem to get increase in popc molecules with equal amount of water on both leaflets. Thanks in advance. I guess that depends on the size of your protein. You should have enough lipds such that the protein doesn't interact with its preriodic image. 90 POPC seem to be a bit to few for that. In my aquaporin simulations, I usually had something like 270 POPE molecules, but if you simulate a smaller protein, less lipids may be sufficient. You may also want to use a hexagonal box which will allow you have less lipids and water. cheers, jochen sudheer babu wrote: Hi gmx-users, whats the number of POPC molecules should be there after inserting protein into popc? In my case 90 popc molecules are there around the protein from 128 molecues which I downloaded from Dr.Tielman's website. Any suggestion will be appreciated Thanks in advance. Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)551 201-2312 -- ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! End of gmx-users Digest, Vol 53, Issue 81 * ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: gmx-users Digest, Vol 53, Issue 82
dear Justin I tried by including lipid.itp,but it was giving error also what to do then with regards prasun ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: gmx-users Digest, Vol 53, Issue 81
sudheer babu wrote: http://www.gromacs.org/mailman/listinfo/gmx-users Thanks to Jochen To increase the lipid molecule number from 128(which downloaded from Dr.Tieleman site) to more than 158, I issued this command genbox -cs 128popc.gro -o out.gro -box 9.2 9.2 6.3 but in the output file it showed unequal amount water molecules on both leaflets, I have tried in changing the box values in many ways but I couldnt able to get. Can any tell me how can I solve this problem to get increase in popc molecules with equal amount of water on both leaflets. There are a couple options. 1. Start with a bigger lipid solvent, created with genconf (i.e., genconf -nbox 2 2 1 will give a system that starts with 512 lipids) 2. Use a z dimension that corresponds to the original POPC bilayer. There are two POPC structures available at Tieleman's site, neither of which have a vertical box dimension of 6.3. So, unless you have made some modifications to the dimensions of the box, you should start by trying the original z box size, if it will adequately accommodate your system. If your box size is incorrect, genbox tries to overlay more of the solvent box into your system, which is probably why you're getting an uneven distribution of water. 3. Make sure your system is centered within the box. -Justin Thanks in advance. I guess that depends on the size of your protein. You should have enough lipds such that the protein doesn't interact with its preriodic image. 90 POPC seem to be a bit to few for that. In my aquaporin simulations, I usually had something like 270 POPE molecules, but if you simulate a smaller protein, less lipids may be sufficient. You may also want to use a hexagonal box which will allow you have less lipids and water. cheers, jochen sudheer babu wrote: Hi gmx-users, whats the number of POPC molecules should be there after inserting protein into popc? In my case 90 popc molecules are there around the protein from 128 molecues which I downloaded from Dr.Tielman's website. Any suggestion will be appreciated Thanks in advance. Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de http://gwdg.de Tel.: +49 (0)551 201-2312 -- ___ gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! End of gmx-users Digest, Vol 53, Issue 81 * ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: gmx-users Digest, Vol 53, Issue 82
prasun kumar wrote: dear Justin I tried by including lipid.itp,but it was giving error also what to do then with regards If you #include lipid.itp then you are not doing what I have said. You must append the parameters from lipid.itp into the force field file that you are using. For example: WRONG: #include ffgmx.itp #include lipid.itp #include dppc.itp RIGHT: #include ffgmx_lipid.itp ; modify ffgmxnb.itp and ffgmxbon.itp to include ; lipid.itp parameters #include dppc.itp -Justin prasun ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] POPC number
I guess that depends on the size of your protein. You should have enough lipds such that the protein doesn't interact with its preriodic image. 90 POPC seem to be a bit to few for that. In my aquaporin simulations, I usually had something like 270 POPE molecules, but if you simulate a smaller protein, less lipids may be sufficient. You may also want to use a hexagonal box which will allow you have less lipids and water. A hexagonal box? Great. How does one go about constructing that? Is this a cylinder-like box with hexagonal shape or just a triclinic one? In the triclinic case, does the PBC membrane turn out as it should? Thanks, Chris. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] POPC number
[EMAIL PROTECTED] wrote: I guess that depends on the size of your protein. You should have enough lipds such that the protein doesn't interact with its preriodic image. 90 POPC seem to be a bit to few for that. In my aquaporin simulations, I usually had something like 270 POPE molecules, but if you simulate a smaller protein, less lipids may be sufficient. You may also want to use a hexagonal box which will allow you have less lipids and water. A hexagonal box? Great. How does one go about constructing that? Is this a cylinder-like box with hexagonal shape or just a triclinic one? In the triclinic case, does the PBC membrane turn out as it should? Hey Chris, a hexagonal box is a special case of a triclinic one: Here we go: echo CRYST1 90.0 90.0 40.00 90.00 90.00 60.0 P 1 1 x.pdb genbox -cp x.pdb -cs tip4p -o filled.pdb echo 0|trjconv -f filled.pdb -o compact.pdb -ur compact -s filled.pdb pymol compact.pdb Have fun, Jochen Thanks, Chris. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)551 201-2312 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] POPC number
[EMAIL PROTECTED] wrote: I guess that depends on the size of your protein. You should have enough lipds such that the protein doesn't interact with its preriodic image. 90 POPC seem to be a bit to few for that. In my aquaporin simulations, I usually had something like 270 POPE molecules, but if you simulate a smaller protein, less lipids may be sufficient. You may also want to use a hexagonal box which will allow you have less lipids and water. A hexagonal box? Great. How does one go about constructing that? Is this a cylinder-like box with hexagonal shape or just a triclinic one? In the triclinic case, does the PBC membrane turn out as it should? And yes, the PBCs work just fine, as expected from any triclinic box. cheer, jochen Thanks, Chris. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php . -- Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)551 201-2312 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] still system exploid
Dear gmx user I tried everything that you offer me to run my solution. I tried to assess my system by ngmx before running. I realized that my system is exploided befor starting EM. I tried the followinf mdp files: 1-;Enegry minimization cpp = cpp define = -DPSRES integrator = steep emtol = 1000 emstep = 0.001 nsteps = 10 nstenergy = 10 nstxtcout = 10 nstxout = 10 nstcgsteep = 1000 ;steps nstlist = 5 ns_type = grid rlist = 1.0 coulombtype = cut-off rcoulomb= 1.8 vdwtype = cut-off rvdw= 1.0 pbc = xyz tcoupl = berendsen tc_grps = protein tau_t = 0.1 ref_t = 0 pcoupl = berendsen pcoupltype = isotropic tau_p = 1.0 compressibility = 4.6e-5 ref_p = 1.0 constraints = all-bonds constraint_algorithm= shake unconstrained_start = yes lincs_order = 4 lincs_iter = 8 ;freezegrps = Protein POPC ;freezedim = N N NN N N gen-vel = yes gen-temp= 0 2- Enegry minimization cpp = cpp define = -DPOSRES integrator = steep emtol = 1000 emstep = 0.001 nsteps = 10 nstenergy = 10 nstxtcout = 10 nstxout = 10 nstcgsteep = 1000 ;steps nstlist = 5 ns_type = grid rlist = 1.0 coulombtype = cut-off rcoulomb= 1.8 vdwtype = cut-off rvdw= 1.0 pbc = xyz tcoupl = berendsen tc_grps = system tau_t = 0.1 ref_t = 0 pcoupl = berendsen pcoupltype = isotropic tau_p = 1.0 compressibility = 4.6e-5 ref_p = 1.0 constraints = all-bonds constraint_algorithm= shake unconstrained_start = yes lincs_order = 4 lincs_iter = 8 ~ 3- title= Yo cpp = cpp include = define = -DPOSRES ; RUN CONTROL PARAMETERS integrator = l-bfgs ; Start time and timestep in ps tinit= 0 dt = 0.001 nsteps = 1 ; For exact run continuation or redoing part of a run init_step= 0 ; mode for center of mass motion removal comm-mode= Angular ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= Protein ; LANGEVIN DYNAMICS OPTIONS ; Temperature, friction coefficient (amu/ps) and random seed bd-temp = 300 300 bd-fric = 0 ld-seed = 1993 ; ENERGY MINIMIZATION OPTIONS ; Force tolerance and initial step-size emtol= 100 emstep = 0.01 ; Max number of iterations in relax_shells niter= 20 ; Step size (1/ps^2) for minimization of flexible constraints fcstep = 0 ; Frequency of steepest descents steps when doing CG nstcgsteep = 1000 nbfgscorr= 100 ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 1000 nstvout = 1000 nstfout = 0 ; Checkpointing helps you continue after crashes nstcheckpoint= 1000 ; Output frequency for energies to log file and energy file nstlog = 500 nstenergy= 500 ; Output frequency and precision for xtc file nstxtcout= 500 59,1 Top nstxtcout= 500 xtc-precision= 500 ; This selects the subset of atoms for the xtc file. You can ; select multiple groups. By default all atoms will be written. xtc-grps = ; Selection of energy groups energygrps = ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 5 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = xyz ; nblist cut-off rlist= 1.0 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.0 ; Dielectric constant (DC) for cut-off or DC of reaction field epsilon-r= 1 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw-switch = 0 rvdw = 1.2 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; FFT
Re: [gmx-users] still system exploid
What kind of solvent are you using, anyway? Your original post said it was an organic solvent, but in one of your .mdp files you've got POPC, which would imply a membrane. What kind of system are we dealing with? The bottom line is that you have severe atomic overlap, and you might be able to get some clue from the LINCS warnings (which I believe you quoted before) as to where things start to fall apart. If solvent atoms near the protein are the problem, you could temporarily increase the VDW radius of, say, carbon during the genbox stage, and increase your box size slightly (since the solvent will contract during a simulation). A bit of trial and error may be in order there. -Justin Morteza Khabiri wrote: Dear gmx user I tried everything that you offer me to run my solution. I tried to assess my system by ngmx before running. I realized that my system is exploided befor starting EM. I tried the followinf mdp files: 1-;Enegry minimization cpp = cpp define = -DPSRES integrator = steep emtol = 1000 emstep = 0.001 nsteps = 10 nstenergy = 10 nstxtcout = 10 nstxout = 10 nstcgsteep = 1000 ;steps nstlist = 5 ns_type = grid rlist = 1.0 coulombtype = cut-off rcoulomb= 1.8 vdwtype = cut-off rvdw= 1.0 pbc = xyz tcoupl = berendsen tc_grps = protein tau_t = 0.1 ref_t = 0 pcoupl = berendsen pcoupltype = isotropic tau_p = 1.0 compressibility = 4.6e-5 ref_p = 1.0 constraints = all-bonds constraint_algorithm= shake unconstrained_start = yes lincs_order = 4 lincs_iter = 8 ;freezegrps = Protein POPC ;freezedim = N N NN N N gen-vel = yes gen-temp= 0 2- Enegry minimization cpp = cpp define = -DPOSRES integrator = steep emtol = 1000 emstep = 0.001 nsteps = 10 nstenergy = 10 nstxtcout = 10 nstxout = 10 nstcgsteep = 1000 ;steps nstlist = 5 ns_type = grid rlist = 1.0 coulombtype = cut-off rcoulomb= 1.8 vdwtype = cut-off rvdw= 1.0 pbc = xyz tcoupl = berendsen tc_grps = system tau_t = 0.1 ref_t = 0 pcoupl = berendsen pcoupltype = isotropic tau_p = 1.0 compressibility = 4.6e-5 ref_p = 1.0 constraints = all-bonds constraint_algorithm= shake unconstrained_start = yes lincs_order = 4 lincs_iter = 8 ~ 3- title= Yo cpp = cpp include = define = -DPOSRES ; RUN CONTROL PARAMETERS integrator = l-bfgs ; Start time and timestep in ps tinit= 0 dt = 0.001 nsteps = 1 ; For exact run continuation or redoing part of a run init_step= 0 ; mode for center of mass motion removal comm-mode= Angular ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= Protein ; LANGEVIN DYNAMICS OPTIONS ; Temperature, friction coefficient (amu/ps) and random seed bd-temp = 300 300 bd-fric = 0 ld-seed = 1993 ; ENERGY MINIMIZATION OPTIONS ; Force tolerance and initial step-size emtol= 100 emstep = 0.01 ; Max number of iterations in relax_shells niter= 20 ; Step size (1/ps^2) for minimization of flexible constraints fcstep = 0 ; Frequency of steepest descents steps when doing CG nstcgsteep = 1000 nbfgscorr= 100 ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 1000 nstvout = 1000 nstfout = 0 ; Checkpointing helps you continue after crashes nstcheckpoint= 1000 ; Output frequency for energies to log file and energy file nstlog = 500 nstenergy= 500 ; Output frequency and precision for xtc file nstxtcout= 500 59,1 Top nstxtcout= 500 xtc-precision= 500 ; This selects the subset of atoms for the xtc file. You can ; select multiple groups. By default all atoms will be written. xtc-grps = ; Selection of energy groups energygrps = ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 5 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = xyz ; nblist
[gmx-users] infinite CNT and segmentation fault
Hello, I try to simulate infinite nanotube. The bonds in topology are as follows: 1 2 1 1.42e-01 4.00e+05 1.42e-01 4.00e+05 131 1 1.40e-01 4.00e+05 1.40e-01 4.00e+05 1 1500 1 1.42e-01 4.00e+05 1.42e-01 4.00e+05 232 1 1.44e-01 4.00e+05 1.44e-01 4.00e+05 2 1471 1 1.42e-01 4.00e+05 1.42e-01 4.00e+05 3 4 1 1.42e-01 4.00e+05 1.42e-01 4.00e+05 333 1 1.40e-01 4.00e+05 1.40e-01 4.00e+05 3 1472 1 1.42e-01 4.00e+05 1.42e-01 4.00e+05 434 1 1.44e-01 4.00e+05 1.44e-01 4.00e+05 4 1473 1 1.42e-01 4.00e+05 1.42e-01 4.00e+05 .. .. The coordinates: 1UNK C1 2.312 3.095 0.071 1UNK C2 2.448 3.055 0.071 1UNK C3 2.698 2.922 0.071 1UNK C4 2.807 2.831 0.071 1UNK C5 2.982 2.607 0.071 1UNK C6 3.044 2.480 0.071 1UNK C7 3.112 2.205 0.071 1UNK C8 3.117 2.063 0.071 1UNK C 1495 1.305 2.735 6.101 1UNK C 1496 1.511 2.929 6.101 1UNK C 1497 1.633 3.003 6.101 1UNK C 1498 1.900 3.097 6.101 1UNK C 1499 2.041 3.115 6.101 1UNK C 1500 2.323 3.092 6.101 4.2 4.2 6.17200 The output of mdrun: Back Off! I just backed up md.log to ./#md.log.2# Getting Loaded... Reading file topol.tpr, VERSION 3.3.1 (single precision) Loaded with Money Back Off! I just backed up ener.edr to ./#ener.edr.2# starting mdrun 'ICE' 1000 steps, 0.0 ps. Segmentation fault The distances between images seem to be correct. pbc=full in mdp. Pressure coupling is off. If one runs x2top without '-pbc' everything is OK. What else can be wrong? Can the below warning lead to the crash (grommp): WARNING 2 [file aminoacids.dat, line 1]: Can not exclude the lattice Coulomb energy between energy groups Checking consistency between energy and charge groups... How to overcome it? Thanks. -- Vitaly V. Chaban School of Chemistry National University of Kharkiv Svoboda sq.,4, Kharkiv 61077, Ukraine email: [EMAIL PROTECTED] skype: vvchaban tel.: +38-097-8259698 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Segmentation fault in Gromacs 4.0 beta1
Hi, everyone: I am a beginner for Gromacs. I am using the latest version Gromacs 4.0 beta1. Then I follow the tutorial part: Introduction to MDhttp://md.chem.rug.nl/education/mdcourse/by the Groningen group. Compiling is ok, but I always get the Segmentation fault when I use command : genbox -cp minimized_box.gro -cs spc216.gro -o minimized_water.gro -p aki.top. Also I get the same problem when i try other exercises. Does anyone has same problem like me ? or can anyone give me a hint for that? Thanks in advance. -Xianghong Qi -- Postdoctoral Associate Department of Chemistry University of Pittsburgh Chevron Science Center 219 Parkman Avenue Pittsburgh, PA 15260 Office: 338 EBERLY Phone: 412-383-5400 Some people make the world more special just by being in it. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: Segmentation fault in Gromacs 4.0 beta1
xianghong qi wrote: Hi, everyone: I am a beginner for Gromacs. I am using the latest version Gromacs 4.0 beta1. Then I follow the tutorial part: Introduction to MD http://md.chem.rug.nl/education/mdcourse/ by the Groningen group. Compiling is ok, but I always get the Segmentation fault when I use command : genbox -cp minimized_box.gro -cs spc216.gro -o minimized_water.gro -p aki.top. Also I get the same problem when i try other exercises. Does anyone has same problem like me ? or can anyone give me a hint for that? Thanks in advance. It sounds like your installation is faulty. What architecture are you running on? What compilers did you use? If you are just starting out, it is probably better to use an official release of Gromacs (the latest being 3.3.3), since 4.0beta1 is still in development. -Justin -Xianghong Qi -- Postdoctoral Associate Department of Chemistry University of Pittsburgh Chevron Science Center 219 Parkman Avenue Pittsburgh, PA 15260 Office: 338 EBERLY Phone: 412-383-5400 Some people make the world more special just by being in it. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: still system exploid
I tried everything that you offer me to run my solution. I tried to assess my system by ngmx before running. I realized that my system is exploided befor starting EM. I tried the followinf mdp files: Did you try to decrease the timestep? -- Vitaly V. Chaban School of Chemistry National University of Kharkiv Svoboda sq.,4, Kharkiv 61077, Ukraine email: [EMAIL PROTECTED] skype: vvchaban tel.: +38-097-8259698 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: Segmentation fault in Gromacs 4.0 beta1
Thanks for your response. I followed the instruction in CVS. my architecture is x86-64, and compiler is gcc. thanks. I will try 3.3.3 -Xianghong Qi On Tue, Sep 16, 2008 at 4:02 PM, Justin A. Lemkul [EMAIL PROTECTED] wrote: xianghong qi wrote: Hi, everyone: I am a beginner for Gromacs. I am using the latest version Gromacs 4.0 beta1. Then I follow the tutorial part: Introduction to MD http://md.chem.rug.nl/education/mdcourse/ by the Groningen group. Compiling is ok, but I always get the Segmentation fault when I use command : genbox -cp minimized_box.gro -cs spc216.gro -o minimized_water.gro -p aki.top. Also I get the same problem when i try other exercises. Does anyone has same problem like me ? or can anyone give me a hint for that? Thanks in advance. It sounds like your installation is faulty. What architecture are you running on? What compilers did you use? If you are just starting out, it is probably better to use an official release of Gromacs (the latest being 3.3.3), since 4.0beta1 is still in development. -Justin -Xianghong Qi -- Postdoctoral Associate Department of Chemistry University of Pittsburgh Chevron Science Center 219 Parkman Avenue Pittsburgh, PA 15260 Office: 338 EBERLY Phone: 412-383-5400 Some people make the world more special just by being in it. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Postdoctoral Associate Department of Chemistry University of Pittsburgh Chevron Science Center 219 Parkman Avenue Pittsburgh, PA 15260 Office: 338 EBERLY Phone: 412-383-5400 Some people make the world more special just by being in it. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: Segmentation fault in Gromacs 4.0 beta1
Justin A. Lemkul wrote: xianghong qi wrote: Thanks for your response. I followed the instruction in CVS. my architecture is x86-64, and compiler is gcc. thanks. Be careful to use a compatible gcc version (i.e., not 4.1.x). Bad compilers can often produce nonfunctional executables. -Justin I will try 3.3.3 -Xianghong Qi On Tue, Sep 16, 2008 at 4:02 PM, Justin A. Lemkul [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: xianghong qi wrote: Hi, everyone: I am a beginner for Gromacs. I am using the latest version Gromacs 4.0 beta1. Then I follow the tutorial part: Introduction to MD http://md.chem.rug.nl/education/mdcourse/ by the Groningen group. Compiling is ok, but I always get the Segmentation fault when I use command : genbox -cp minimized_box.gro -cs spc216.gro -o minimized_water.gro -p aki.top. Also I get the same problem when i try other exercises. Does anyone has same problem like me ? or can anyone give me a hint for that? Thanks in advance. It sounds like your installation is faulty. What architecture are you running on? What compilers did you use? If you are just starting out, it is probably better to use an official release of Gromacs (the latest being 3.3.3), since 4.0beta1 is still in development. -Justin -Xianghong Qi -- Postdoctoral Associate Department of Chemistry University of Pittsburgh Chevron Science Center 219 Parkman Avenue Pittsburgh, PA 15260 Office: 338 EBERLY Phone: 412-383-5400 Some people make the world more special just by being in it. ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] mailto:[EMAIL PROTECTED]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant 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://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] mailto:[EMAIL PROTECTED]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Postdoctoral Associate Department of Chemistry University of Pittsburgh Chevron Science Center 219 Parkman Avenue Pittsburgh, PA 15260 Office: 338 EBERLY Phone: 412-383-5400 Some people make the world more special just by being in it. -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] still system exploid
Dear gmxuser, Thanks for your all helps. But still I have problem. As you friend said I increase the vdw and box size and also i decrease the time step till 0.0001 but unfortunately system crash befor EM running. I do check with ngmx. To reply the question that said what is your system? My system is ACETONE + water + protein which i mixed water and protein before and i just put the protein in the solution of ACETONE and water. About mdp that has a popc, I should say that this mdp was fpr my membrane which i used it before and i just change some of the parameter of this file and because the name was not important i did not change it. I am sorry my gro file is big and because of this the gmxmail servic avoid to send it. I will send to privet email. for coulomb i use the followings: 1- coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.0 ; Dielectric constant (DC) for cut-off or DC of reaction field epsilon-r= 1 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw-switch = 0 rvdw = 1.2 2- coulombtype = cut-off rcoulomb= 1.8 vdwtype = cut-off rvdw= 1.0 again thanks Morteza ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Segmentation fault in Gromacs 4.0 beta1
I am a beginner for Gromacs. I am using the latest version Gromacs 4.0 beta1. Then I follow the tutorial part: Introduction to MD http://md.chem.rug.nl/education/mdcourse/ by the Groningen group. Compiling is ok, but I always get the Segmentation fault when I use command : genbox -cp minimized_box.gro -cs spc216.gro -o minimized_water.gro -p aki.top. Also I get the same problem when i try other exercises. Does anyone has same problem like me ? or can anyone give me a hint for that? Thanks in advance. It sounds like your installation is faulty. What architecture are you running on? What compilers did you use? If you are just starting out, it is probably better to use an official release of Gromacs (the latest being 3.3.3), since 4.0beta1 is still in development. -Justin Justin, A few days ago I experienced the same problem with genbox in gmx-4.0-beta. I didn't pay much attention to it since it's just CVS but it actually was permanently present. gmx-4.0 compiled with the same parameters on the same system does not give this error. Xianghong, There's no such problem in gmx-3.3.3 and earlier ones. I would suggest you to use them to avoid much headache. -- Vitaly V. Chaban School of Chemistry National University of Kharkiv Svoboda sq.,4, Kharkiv 61077, Ukraine email: [EMAIL PROTECTED] skype: vvchaban tel.: +38-097-8259698 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re[2]: Segmentation fault in Gromacs 4.0 beta1
I am a beginner for Gromacs. I am using the latest version Gromacs 4.0 beta1. Then I follow the tutorial part: Introduction to MD http://md.chem.rug.nl/education/mdcourse/ by the Groningen group. Compiling is ok, but I always get the Segmentation fault when I use command : genbox -cp minimized_box.gro -cs spc216.gro -o minimized_water.gro -p aki.top. Also I get the same problem when i try other exercises. Does anyone has same problem like me ? or can anyone give me a hint for that? Thanks in advance. It sounds like your installation is faulty. What architecture are you running on? What compilers did you use? If you are just starting out, it is probably better to use an official release of Gromacs (the latest being 3.3.3), since 4.0beta1 is still in development. -Justin VC Justin, VC A few days ago I experienced the same problem with genbox in gmx-4.0-beta. I didn't VC pay much attention to it since it's just CVS but it actually was VC permanently present. VC gmx-4.0 compiled with the same parameters on the same system does not VC give this error. I wanted to say gmx-3.3.3. I'm quite tired today, sorry. -- Vitaly V. Chaban School of Chemistry National University of Kharkiv Svoboda sq.,4, Kharkiv 61077, Ukraine email: [EMAIL PROTECTED] skype: vvchaban tel.: +38-097-8259698 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] dielectric constant of the medium
Hi all, I am doing some coarse-grained simulations, where I have removed the solvent molecules from the system. In order to incorporate the effect of solvent in my simulations, I need to tune the dielectric constant of the medium. Will just changing epsilon_r in the mdp file work or do I need to do some other fancy stuff? Later on, I want to use two different dielectric constants, i.e. a near field value and a far field value. Is there an easy way of doing this or do I need to modify the source code ? I don't understand the reaction field concept well, still will something on that line work ? Thanks, Nazish ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] PBS Script - trjconv Options
Hello, Simple question. I am running constraint pulling and getting the .xtc and .tpr output files in order to create a pdb video using trjconv. I am running simulations on a cluster, and so a pbs script must be submitted with the necessary commands. When using trjconv command, the group must subsequently be specified. Is there any way to modify the below command to also select a specific group (i.e. - 1 for 'Protein'). For example, when using mdrun, the -ff option can be used to specify which forcefield to use. Is there something similar to this with regards to the group selection when using trjconv? Thanks. trjconv -s peptide.tpr -f trajectory.xtc -o pullvideo.pdb __ Venkatesh Hariharan Pennsylvania State University Schreyer Honors College Undergraduate - Bioengineering You must be the change you wish to see in the world. --Mohandas Karamchand Gandhi ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
