Dear Tsjerk,<br><br>Thank you for your reply, I will try to work with PDB format and get back to you.<br><br><div class="gmail_quote">On Wed, Apr 11, 2012 at 12:22 AM, Tsjerk Wassenaar <span dir="ltr"><<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Hi Ramesh,<br>
<br>
Maybe it is easier, and less error-prone, to work in PDB format,<br>
specifying the box as a CRYST1 record. You can use the PDB format<br>
anywhere in your workflow where GRO format is used.<br>
<br>
Cheers,<br>
<br>
Tsjerk<br>
<div class="HOEnZb"><div class="h5"><br>
<br>
On Tue, Apr 10, 2012 at 8:13 PM, ramesh cheerla <<a href="mailto:rameshgromacs@gmail.com">rameshgromacs@gmail.com</a>> wrote:<br>
> Dear Mark,<br>
><br>
> Thank you for reply, sorry for not being very clear, Here my<br>
> doubt is can i use triclinic box for the simulations of the crystal whose<br>
> unit cell is monoclinic. As i said earlier i have tried editconf as<br>
> editconf -f input.gro -o out_box1.gro -bt triclinic -box 3.22 2.608 7.792<br>
> -angles 90 125.4 90<br>
> it gave the following warning<br>
><br>
> WARNING: Triclinic box is too skewed.<br>
><br>
> for clarity here i am sending a part of the output file generated by the<br>
> editconf<br>
> God Rules Over Mankind, Animals, Cosmos and Such<br>
> 6528<br>
> 1PEGA C1 1 -0.025 0.408 -0.045<br>
> 1PEGA C2 2 -0.015 0.326 0.084<br>
> ::::::::::::::::::::::::::::::::::::::::::::::::::::::::;<br>
> 3.22000 2.60800 6.35148 0.00000 0.00000 0.00000 0.00000<br>
> -4.51376 -0.00000<br>
> if i change the angles while using the editconf i observed the following<br>
> changes<br>
><br>
> editconf -f input.gro -o out_box2.gro -bt triclinic -box 3.22 2.608 7.792<br>
> -angles 90 90 125.4<br>
> in this case editconf haven't given any warning and the output as follows<br>
><br>
> God Rules Over Mankind, Animals, Cosmos and Such<br>
> 6528<br>
> 1PEGA C1 1 1.477 0.167 0.675<br>
> 1PEGA C2 2 1.487 0.085 0.804<br>
> ::::::::::::::::::::::::::::::::::::::::::::::::::::::::;<br>
> 3.22000 2.12585 7.79200 0.00000 0.00000 -1.51077 0.00000<br>
> -0.00000 -0.00000<br>
><br>
> Can you please help me in this regard.<br>
><br>
> thank you in advance.<br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
> On Mon, Ap;r 9, 2012 at 11:55 AM, Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br>
> wrote:<br>
>><br>
>> On 9/04/2012 3:22 PM, ramesh cheerla wrote:<br>
>>><br>
>>> Dear Gromacs users,<br>
>>><br>
>>> I am planing to simulate a polymeric crystal in<br>
>>> gromacs, which is of monoclinic unit cell with cell parameters a = 0.805 nm<br>
>>> b = 1.304 nm and c = 1.948 nm and beta = 125.4 deg. my crystal is of 424<br>
>>> type i.e 4 unit cells along 'a' direction '2' unit cells along 'b'<br>
>>> direction and 4 unit cells along 'c' direction.<br>
>>> So my box vector lengths are a = 3.22 nm, b = 2.608 nm, c = 7.792 nm.<br>
>>> I am using editconf to generate box for this crystal as:<br>
>>><br>
>>> editconf -f input.gro -o out_box.gro -bt tric -box 3.22 2.608 7.792<br>
>>> -angles 90 125.4 90<br>
>>><br>
>>> Here i have some doubts:<br>
>>><br>
>>> 1) Am i using the editconf in correct manner for generation of box for<br>
>>> the monoclinic crystal, though the crystal is of monoclinic i am using box<br>
>>> type as triclinic<br>
>>> i haven't found any specific method for the generation of box for the<br>
>>> monoclinic crystal.<br>
>>> 2) Is there any specific method to generate the box for the monoclinic<br>
>>> crystals.<br>
>>> 3) The notations for the lattice parameters of the crystal i.e 'a' , 'b'<br>
>>> , 'c' and angles alpha, beta , gamma used by crystallography and the gromacs<br>
>>> editconf are the same or different, why because if i use editconf as above i<br>
>>> am getting the following warning:<br>
>>><br>
>>> WARNING: Triclinic box is too skewed.<br>
>><br>
>><br>
>> This means equation 3.3 of the manual is not true. Maybe beta should be<br>
>> acute? I've no idea of necessity or convention here.<br>
>><br>
>> Inspecting the whole output of editconf is probably instructive, but<br>
>> you've kept all that information to yourself instead of re-thinking how your<br>
>> repeat post might be constructed so as to make it easier / more likely for<br>
>> people help you. Likewise the final line of out_box.gro. Make sure you have<br>
>> read and understood what documentation is available with editconf -h and in<br>
>> manual section 3.2.<br>
>><br>
>> Mark<br>
>> --<br>
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><br>
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<br>
<br>
</div></div><span class="HOEnZb"><font color="#888888">--<br>
Tsjerk A. Wassenaar, Ph.D.<br>
<br>
post-doctoral researcher<br>
Molecular Dynamics Group<br>
* Groningen Institute for Biomolecular Research and Biotechnology<br>
* Zernike Institute for Advanced Materials<br>
University of Groningen<br>
The Netherlands<br>
</font></span><div class="HOEnZb"><div class="h5">--<br>
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